BioC 3.3: CHECK report for DAPAR on morelia

Package: DAPAR

Version: 1.1.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings DAPAR_1.1.0.tar.gz

StartedAt: 2015-10-22 05:12:23 -0400 (Thu, 22 Oct 2015)

EndedAt: 2015-10-22 05:14:48 -0400 (Thu, 22 Oct 2015)

EllapsedTime: 145.5 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_1.1.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/DAPAR.Rcheck’
* using R Under development (unstable) (2015-10-08 r69496)
* 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 ‘1.1.0’
* 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 ... [12s/13s] 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’
Undefined global functions or variables:
  exprs exprs<- 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 ... [15s/14s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [6s/6s]
 [6s/6s] 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-3.3-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	0.152	0.013	0.165
corrMatrixD	0.288	0.013	0.301
createMSnset	0.136	0.013	0.149
densityPlotD	0.113	0.009	0.122
diffAna	0.561	0.059	0.619
diffAnaComputeFDR	0.245	0.012	0.257
diffAnaGetSignificant	0.133	0.008	0.141
diffAnaLimma	0.139	0.009	0.147
diffAnaSave	0.140	0.009	0.149
diffAnaVolcanoplot	0.129	0.008	0.138
diffAnaWelch	0.097	0.006	0.103
getIndicesConditions	0.115	0.007	0.124
getNumberOfEmptyLines	0.148	0.009	0.161
getPaletteForLabels	0.111	0.007	0.118
getPourcentageOfMV	0.128	0.010	0.137
heatmapD	0.042	0.002	0.044
mvFilter	0.245	0.010	0.255
mvHisto	0.136	0.008	0.144
mvImage	2.688	0.091	2.770
mvImputation	0.141	0.008	0.149
mvPerLinesHisto	0.107	0.007	0.116
mvPieChart	0.135	0.008	0.143
mvTypePlot	0.23	0.01	0.24
normalizeD	0.150	0.010	0.159
varianceDistD	0.440	0.020	0.463
writeMSnsetToExcel	2.420	0.142	1.693