BioC 3.2: CHECK report for DAPAR on oaxaca

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: 2016-04-22 23:23:58 -0700 (Fri, 22 Apr 2016)

EndedAt: 2016-04-22 23:29:31 -0700 (Fri, 22 Apr 2016)

EllapsedTime: 333.8 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 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (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 ... [16s/17s] 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 ... [159s/158s] OK
Examples with CPU or elapsed time > 5s
           user system elapsed
mvImage 140.632  0.492 141.281
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [9s/9s]
 [10s/10s] 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	0.161	0.024	0.186
corrMatrixD	0.399	0.016	0.470
createMSnset	0.188	0.008	0.196
densityPlotD	0.160	0.014	0.281
diffAna	0.710	0.061	0.770
diffAnaComputeFDR	0.250	0.017	0.267
diffAnaGetSignificant	0.133	0.012	0.145
diffAnaLimma	0.153	0.009	0.161
diffAnaSave	0.125	0.010	0.136
diffAnaVolcanoplot	0.136	0.011	0.147
diffAnaWelch	0.133	0.011	0.145
getIndicesConditions	0.139	0.011	0.150
getNumberOfEmptyLines	0.147	0.012	0.160
getPaletteForLabels	0.136	0.013	0.148
getPourcentageOfMV	0.147	0.011	0.157
heatmapD	0.481	0.013	0.495
mvFilter	0.234	0.015	0.250
mvHisto	0.168	0.016	0.194
mvImage	140.632	0.492	141.281
mvImputation	0.151	0.021	0.171
mvPerLinesHisto	0.152	0.021	0.177
mvPieChart	0.126	0.018	0.146
mvTypePlot	0.296	0.023	0.323
normalizeD	0.135	0.020	0.156
varianceDistD	0.581	0.022	0.606
writeMSnsetToExcel	2.878	0.164	2.082