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: 2015-10-27 02:56:19 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 02:59:39 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 199.9 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 (2015-08-14)
* 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 ... [18s/19s] 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 ... [20s/19s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [8s/8s]
 [8s/8s] 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	0.146	0.018	0.164
corrMatrixD	0.375	0.014	0.389
createMSnset	0.203	0.011	0.213
densityPlotD	0.148	0.012	0.161
diffAna	0.572	0.049	0.621
diffAnaComputeFDR	0.262	0.015	0.278
diffAnaGetSignificant	0.140	0.010	0.153
diffAnaLimma	0.140	0.011	0.152
diffAnaSave	0.138	0.011	0.149
diffAnaVolcanoplot	0.143	0.012	0.160
diffAnaWelch	0.136	0.010	0.147
getIndicesConditions	0.139	0.012	0.151
getNumberOfEmptyLines	0.146	0.011	0.160
getPaletteForLabels	0.134	0.011	0.148
getPourcentageOfMV	0.156	0.011	0.174
heatmapD	0.038	0.001	0.040
mvFilter	0.490	0.016	0.512
mvHisto	0.144	0.011	0.158
mvImage	3.326	0.109	3.431
mvImputation	0.144	0.010	0.153
mvPerLinesHisto	0.148	0.012	0.163
mvPieChart	0.151	0.011	0.163
mvTypePlot	0.260	0.012	0.273
normalizeD	0.119	0.010	0.129
varianceDistD	0.521	0.014	0.540
writeMSnsetToExcel	2.578	0.156	1.807