BioC 3.3: CHECK report for DAPAR on linux2.bioconductor.org

Package: DAPAR

Version: 1.1.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings DAPAR_1.1.0.tar.gz

StartedAt: 2015-10-27 03:11:45 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 03:13:56 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 130.5 seconds

RetCode: 0

Status:  OK

CheckDir: DAPAR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings DAPAR_1.1.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/DAPAR.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* using platform: x86_64-pc-linux-gnu (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 ... [11s/11s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [13s/12s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [5s/5s]
 [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
  ‘/home/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	0.108	0.004	0.112
corrMatrixD	0.247	0.008	0.256
createMSnset	0.127	0.008	0.135
densityPlotD	0.119	0.000	0.119
diffAna	0.396	0.032	0.429
diffAnaComputeFDR	0.188	0.000	0.188
diffAnaGetSignificant	0.094	0.000	0.097
diffAnaLimma	0.093	0.004	0.096
diffAnaSave	0.117	0.000	0.118
diffAnaVolcanoplot	0.102	0.000	0.102
diffAnaWelch	0.095	0.000	0.096
getIndicesConditions	0.096	0.000	0.096
getNumberOfEmptyLines	0.101	0.000	0.101
getPaletteForLabels	0.097	0.000	0.096
getPourcentageOfMV	0.107	0.000	0.107
heatmapD	0.029	0.000	0.029
mvFilter	0.166	0.000	0.166
mvHisto	0.093	0.008	0.101
mvImage	2.639	0.016	2.658
mvImputation	0.111	0.000	0.112
mvPerLinesHisto	0.106	0.004	0.110
mvPieChart	0.103	0.004	0.107
mvTypePlot	0.176	0.004	0.180
normalizeD	0.095	0.004	0.099
varianceDistD	0.309	0.008	0.318
writeMSnsetToExcel	1.781	0.040	1.058