BioC 3.3: CHECK report for DAPAR on oaxaca

Package: DAPAR

Version: 1.4.8

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings DAPAR_1.4.8.tar.gz

StartedAt: 2016-10-13 00:44:49 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 00:48:22 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 213.7 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_1.4.8.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/DAPAR.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.4.8’
* 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
Examples with CPU or elapsed time > 5s
              user system elapsed
TopnPeptides 2.869  2.421   1.709
* 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	0.511	0.261	0.805
BuildColumnToProteinDataset	0.347	0.017	0.364
BuildSparseAdjacencyMatrix	0.210	0.085	0.296
CountPep	0.463	0.229	0.692
GraphPepProt	0.342	0.013	0.356
MeanPeptides	0.914	0.754	1.442
MeanPeptidesSpeedUp	0.095	0.043	0.136
SumPeptides	1.672	1.431	1.088
SumPeptidesSpeedUp	0.076	0.040	0.115
TopnPeptides	2.869	2.421	1.709
boxPlotD	0.050	0.014	0.064
compareNormalizationD	0.057	0.007	0.063
corrMatrixD	0.316	0.032	0.349
createMSnset	0.205	0.014	0.219
deleteLinesFromIndices	0.037	0.005	0.043
densityPlotD	0.058	0.006	0.066
diffAna	0.282	0.025	0.307
diffAnaComputeFDR	0.086	0.007	0.094
diffAnaGetSignificant	0.042	0.004	0.047
diffAnaLimma	0.037	0.005	0.042
diffAnaSave	0.036	0.004	0.040
diffAnaVolcanoplot	0.045	0.005	0.050
diffAnaWelch	0.036	0.004	0.041
getIndicesConditions	0.037	0.004	0.041
getIndicesOfLinesToRemove	0.033	0.005	0.037
getNumberOf	0.035	0.004	0.039
getNumberOfEmptyLines	0.040	0.005	0.044
getPaletteForLabels	0.036	0.005	0.041
getPaletteForReplicates	0.035	0.005	0.041
getPourcentageOfMV	0.036	0.005	0.041
getProcessingInfo	0.037	0.005	0.043
getProteinsStats	0.379	0.048	0.428
heatmap.DAPAR	0.226	0.021	0.248
heatmapD	0.250	0.020	0.283
limmaCompleteTest	0.071	0.004	0.075
mvFilter	0.076	0.003	0.080
mvFilterFromIndices	0.030	0.004	0.033
mvFilterGetIndices	0.046	0.008	0.054
mvHisto	0.072	0.007	0.091
mvImage	0.220	0.006	0.226
mvImputation	0.074	0.024	0.097
mvPerLinesHisto	0.051	0.004	0.057
mvPerLinesHistoPerCondition	0.038	0.004	0.042
mvTypePlot	0.108	0.005	0.113
normalizeD	0.048	0.019	0.066
pepAgregate	0.074	0.008	0.083
pepAgregateSpeedUp	0.116	0.008	0.124
proportionConRev	0.083	0.005	0.088
removeLines	0.035	0.003	0.038
topMaxUsingPartialSortIndices	0.001	0.000	0.001
varianceDistD	0.030	0.003	0.033
wrapper.boxPlotD	0.039	0.004	0.045
wrapper.compareNormalizationD	0.045	0.003	0.063
wrapper.corrMatrixD	0.232	0.003	0.238
wrapper.densityPlotD	0.053	0.004	0.058
wrapper.diffAnaLimma	0.031	0.003	0.034
wrapper.diffAnaWelch	0.032	0.003	0.035
wrapper.heatmapD	0.220	0.013	0.235
wrapper.mvHisto	0.065	0.006	0.081
wrapper.mvImage	0.222	0.008	0.231
wrapper.mvImputation	0.058	0.004	0.062
wrapper.mvPerLinesHisto	0.050	0.004	0.056
wrapper.mvPerLinesHistoPerCondition	0.039	0.004	0.043
wrapper.mvTypePlot	0.092	0.005	0.113
wrapper.normalizeD	0.042	0.004	0.046
wrapper.varianceDistD	0.243	0.008	0.253
wrapperCalibrationPlot	0.034	0.003	0.038
writeMSnsetToExcel	2.003	0.087	1.922