BioC 3.2: CHECK report for DAPAR on perceval

Package: DAPAR

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings DAPAR_1.0.0.tar.gz

StartedAt: 2015-10-20 07:12:12 -0400 (Tue, 20 Oct 2015)

EndedAt: 2015-10-20 07:16:39 -0400 (Tue, 20 Oct 2015)

EllapsedTime: 267.5 seconds

RetCode: 0

Status:  OK

CheckDir: DAPAR.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 DAPAR_1.0.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/DAPAR.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DAPAR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DAPAR’ version ‘1.0.0’
* 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 ‘DAPAR’ can be installed ... [26s/28s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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
boxPlotD: no visible global function definition for ‘exprs’
boxPlotD: no visible global function definition for ‘pData’
corrMatrixD: no visible global function definition for ‘pData’
corrMatrixD: no visible global function definition for ‘exprs’
createMSnset: no visible global function definition for ‘exprs<-’
createMSnset: no visible global function definition for ‘exprs’
densityPlotD: no visible global function definition for ‘pData’
densityPlotD: no visible global function definition for ‘exprs’
diffAna: no visible global function definition for ‘exprs’
diffAnaLimma: no visible global function definition for ‘exprs’
diffAnaLimma: no visible global function definition for ‘pData’
diffAnaWelch: no visible global function definition for ‘exprs’
getIndicesConditions: no visible global function definition for ‘pData’
getNumberOfEmptyLines: no visible global function definition for
  ‘exprs’
getPaletteForLabels: no visible global function definition for ‘pData’
getPourcentageOfMV: no visible global function definition for ‘exprs’
heatmapD: no visible global function definition for ‘exprs’
mvFilter: no visible global function definition for ‘pData’
mvFilter: no visible global function definition for ‘exprs’
mvHisto: no visible global function definition for ‘pData’
mvHisto: no visible global function definition for ‘exprs’
mvImage: no visible global function definition for ‘pData’
mvImage: no visible global function definition for ‘exprs’
mvImage: no visible global function definition for ‘exprs<-’
mvImputation: no visible global function definition for ‘exprs’
mvImputation: no visible global function definition for ‘exprs<-’
mvPerLinesHisto: no visible global function definition for ‘exprs’
mvPerLinesHisto: no visible global function definition for ‘pData’
mvTypePlot: no visible global function definition for ‘exprs’
mvTypePlot: no visible global function definition for ‘pData’
normalizeD: no visible global function definition for ‘exprs’
normalizeD: no visible global function definition for ‘exprs<-’
normalizeD: no visible global function definition for ‘pData’
varianceDistD: no visible global function definition for ‘pData’
varianceDistD: no visible global function definition for ‘exprs’
writeMSnsetToExcel: no visible global function definition for ‘exprs’
writeMSnsetToExcel: no visible global function definition for ‘pData’
* 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/24s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [11s/11s]
 [11s/12s] 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/DAPAR.Rcheck/00check.log’
for details.

* installing *source* package ‘DAPAR’ ...
** 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 (DAPAR)

name	user	system	elapsed
boxPlotD	0.169	0.024	0.194
corrMatrixD	0.382	0.012	0.424
createMSnset	0.179	0.011	0.189
densityPlotD	0.166	0.014	0.181
diffAna	0.812	0.062	1.034
diffAnaComputeFDR	0.282	0.013	0.296
diffAnaGetSignificant	0.151	0.011	0.165
diffAnaLimma	0.141	0.010	0.152
diffAnaSave	0.137	0.010	0.147
diffAnaVolcanoplot	0.145	0.010	0.160
diffAnaWelch	0.142	0.009	0.154
getIndicesConditions	0.136	0.009	0.146
getNumberOfEmptyLines	0.145	0.009	0.155
getPaletteForLabels	0.139	0.009	0.149
getPourcentageOfMV	0.167	0.013	0.183
heatmapD	0.046	0.003	0.050
mvFilter	0.577	0.018	0.594
mvHisto	0.143	0.011	0.156
mvImage	4.061	0.254	4.323
mvImputation	0.169	0.012	0.182
mvPerLinesHisto	0.162	0.012	0.252
mvPieChart	0.154	0.010	0.170
mvTypePlot	0.292	0.014	0.383
normalizeD	0.143	0.009	0.153
varianceDistD	0.522	0.028	0.882
writeMSnsetToExcel	3.562	0.392	3.606