BioC 3.4: CHECK report for DAPAR on morelia

Package: DAPAR

Version: 1.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings DAPAR_1.6.0.tar.gz

StartedAt: 2017-04-15 00:49:00 -0700 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 00:52:28 -0700 (Sat, 15 Apr 2017)

EllapsedTime: 207.9 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_1.6.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/DAPAR.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.6.0’
* 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 ... 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 ... OK
* 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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 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: OK

* 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
BuildAdjacencyMatrix	0.493	0.101	0.596
BuildColumnToProteinDataset	0.329	0.015	0.345
CountPep	0.197	0.070	0.269
GraphPepProt	0.313	0.007	0.319
MeanPeptides	0.082	0.030	0.113
SumPeptides	0.068	0.034	0.102
TopnPeptides	1.969	0.075	2.069
boxPlotD	0.049	0.007	0.092
compareNormalizationD	0.056	0.007	0.124
corrMatrixD	0.345	0.013	0.439
createMSnset	0.178	0.001	0.179
deleteLinesFromIndices	0.036	0.005	0.040
densityPlotD	0.060	0.004	0.087
diffAna	0.289	0.026	0.314
diffAnaComputeFDR	0.103	0.008	0.110
diffAnaGetSignificant	0.029	0.003	0.032
diffAnaLimma	0.041	0.004	0.045
diffAnaSave	0.042	0.004	0.045
diffAnaVolcanoplot	0.043	0.005	0.062
diffAnaWelch	0.037	0.004	0.042
getIndicesConditions	0.042	0.004	0.047
getIndicesOfLinesToRemove	0.039	0.004	0.044
getNumberOf	0.036	0.005	0.041
getNumberOfEmptyLines	0.044	0.005	0.048
getPaletteForLabels	0.041	0.005	0.046
getPaletteForReplicates	0.040	0.004	0.044
getPourcentageOfMV	0.041	0.004	0.045
getProcessingInfo	0.040	0.005	0.046
getProteinsStats	0.065	0.010	0.076
heatmap.DAPAR	0.212	0.018	0.270
heatmapD	0.519	0.019	0.836
limmaCompleteTest	0.069	0.004	0.073
mvFilter	0.065	0.004	0.068
mvFilterFromIndices	0.038	0.004	0.042
mvFilterGetIndices	0.042	0.008	0.050
mvHisto	0.073	0.009	0.365
mvImage	0.208	0.005	0.236
mvImputation	0.079	0.023	0.102
mvPerLinesHisto	0.047	0.004	0.135
mvPerLinesHistoPerCondition	0.041	0.005	0.061
mvTypePlot	0.106	0.006	0.129
normalizeD	0.059	0.019	0.103
pepAgregate	0.127	0.013	0.140
proportionConRev	0.080	0.005	0.107
removeLines	0.039	0.003	0.067
varianceDistD	0.031	0.003	0.034
violinPlotD	0.155	0.009	0.462
wrapper.boxPlotD	0.037	0.004	0.056
wrapper.compareNormalizationD	0.054	0.005	0.073
wrapper.corrMatrixD	0.263	0.004	0.306
wrapper.densityPlotD	0.070	0.004	0.089
wrapper.diffAnaLimma	0.033	0.003	0.036
wrapper.diffAnaWelch	0.041	0.004	0.044
wrapper.heatmapD	0.210	0.017	0.271
wrapper.mvHisto	0.054	0.009	0.337
wrapper.mvImage	0.192	0.007	0.223
wrapper.mvImputation	0.059	0.006	0.066
wrapper.mvPerLinesHisto	0.047	0.007	0.067
wrapper.mvPerLinesHistoPerCondition	0.031	0.006	0.052
wrapper.mvTypePlot	0.098	0.008	0.122
wrapper.normalizeD	0.046	0.007	0.053
wrapper.varianceDistD	0.261	0.008	0.386
wrapper.violinPlotD	0.159	0.009	0.170
wrapperCalibrationPlot	0.036	0.005	0.042
writeMSnsetToExcel	0.394	0.041	1.590