Package: DAPAR

Version: 1.10.4

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings DAPAR_1.10.4.tar.gz

StartedAt: 2018-04-12 02:31:47 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 02:39:03 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 436.2 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_1.10.4.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/DAPAR.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.10.4’
* 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 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
wrapper.compareNormalizationD_HC 33.898  0.125  34.893
compareNormalizationD_HC         31.951  0.151  32.875
wrapper.dapar.impute.mi          22.480  0.549  23.678
enrich_GO                        14.881  0.814  16.104
group_GO                         11.134  0.702  12.135
* 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
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (DAPAR)

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(DAPAR)

> 
> test_check("DAPAR")
Procedure of Benjamini-Hochberg is used. pi0 is fixed to 1.
1 2 3 4 5   
5 2 2 4 1 0 
1 2 3 4 5   
5 2 2 4 1 0 
1 2 3 4 5   
5 2 2 4 1 0 
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 125 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 19.490   0.478  20.667 

name	user	system	elapsed
BuildAdjacencyMatrix	0.993	0.112	1.128
BuildColumnToProteinDataset	1.891	0.047	1.983
BuildColumnToProteinDataset_par	1.111	0.188	1.387
CVDistD	4.079	0.097	4.363
CVDistD_HC	2.638	0.041	2.751
CountPep	0.657	0.111	0.786
GraphPepProt	0.427	0.022	0.462
MeanPeptides	0.675	0.040	0.734
StringBasedFiltering	0.899	0.018	0.946
SumPeptides	0.332	0.037	0.375
TopnPeptides	2.286	0.065	2.403
boxPlotD	1.076	0.006	1.108
boxPlotD_HC	1.788	0.037	1.870
compareNormalizationD	0.393	0.016	0.415
compareNormalizationD_HC	31.951	0.151	32.875
corrMatrixD	1.802	0.044	1.884
corrMatrixD_HC	0.369	0.021	0.416
createMSnset	1.185	0.018	1.244
deleteLinesFromIndices	0.328	0.007	0.344
densityPlotD	0.340	0.008	0.357
densityPlotD_HC	1.522	0.025	1.578
diffAna	0.573	0.022	0.600
diffAnaComputeFDR	1.230	0.006	1.280
diffAnaGetSignificant	0.294	0.003	0.307
diffAnaLimma	0.361	0.015	0.386
diffAnaSave	0.315	0.004	0.325
diffAnaVolcanoplot_rCharts	0.884	0.031	0.934
diffAnaWelch	0.293	0.005	0.306
enrich_GO	14.881	0.814	16.104
getIndicesConditions	0.256	0.003	0.262
getIndicesOfLinesToRemove	0.250	0.004	0.263
getNumberOf	0.257	0.004	0.268
getNumberOfEmptyLines	0.280	0.004	0.295
getPaletteForLabels	0.254	0.004	0.265
getPaletteForLabels_HC	0.258	0.004	0.262
getPaletteForReplicates	0.267	0.004	0.272
getPaletteForReplicates_HC	0.256	0.004	0.263
getPourcentageOfMV	0.296	0.006	0.318
getProcessingInfo	0.330	0.006	0.386
getProteinsStats	0.315	0.012	0.339
getQuantile4Imp	0.280	0.005	0.289
group_GO	11.134	0.702	12.135
heatmap.DAPAR	0.639	0.015	0.660
heatmapD	1.323	0.047	1.387
impute.detQuant	0.677	0.335	1.061
impute.pa2	0.357	0.004	0.363
limmaCompleteTest	0.327	0.003	0.331
mvFilter	0.291	0.006	0.303
mvFilterFromIndices	0.288	0.004	0.296
mvFilterGetIndices	0.375	0.085	0.472
mvHisto	0.273	0.006	0.292
mvHisto_HC	0.309	0.019	0.330
mvImage	3.538	0.027	3.633
mvImputation	0.253	0.008	0.276
mvPerLinesHisto	0.340	0.014	0.366
mvPerLinesHistoPerCondition	0.293	0.006	0.304
mvPerLinesHistoPerCondition_HC	0.325	0.020	0.354
mvPerLinesHisto_HC	0.310	0.025	0.343
mvTypePlot	1.548	0.028	1.623
my_hc_ExportMenu	0.165	0.048	0.218
my_hc_chart	0.136	0.051	0.193
nonzero	0.103	0.000	0.106
normalizeD	0.316	0.024	0.350
normalizeD2	0.338	0.026	0.369
pepAgregate	0.369	0.010	0.381
proportionConRev_HC	0.047	0.014	0.062
removeLines	0.260	0.002	0.275
translatedRandomBeta	0.003	0.003	0.007
violinPlotD	2.307	0.021	2.377
wrapper.CVDistD	3.512	0.024	3.594
wrapper.CVDistD_HC	2.340	0.025	2.398
wrapper.boxPlotD	0.280	0.005	0.289
wrapper.boxPlotD_HC	1.355	0.039	1.432
wrapper.compareNormalizationD	0.403	0.018	0.425
wrapper.compareNormalizationD_HC	33.898	0.125	34.893
wrapper.corrMatrixD	2.071	0.016	2.130
wrapper.corrMatrixD_HC	0.442	0.019	0.471
wrapper.dapar.impute.mi	22.480	0.549	23.678
wrapper.densityPlotD	0.310	0.013	0.326
wrapper.densityPlotD_HC	1.545	0.022	1.591
wrapper.diffAnaLimma	0.293	0.002	0.302
wrapper.diffAnaWelch	0.292	0.003	0.307
wrapper.heatmapD	1.322	0.024	1.372
wrapper.impute.detQuant	0.259	0.004	0.263
wrapper.impute.pa	0.369	0.007	0.377
wrapper.impute.pa2	0.323	0.004	0.331
wrapper.mvHisto	0.286	0.007	0.299
wrapper.mvHisto_HC	0.228	0.003	0.232
wrapper.mvImage	3.057	0.020	3.135
wrapper.mvImputation	0.276	0.003	0.285
wrapper.mvPerLinesHisto	0.352	0.012	0.372
wrapper.mvPerLinesHistoPerCondition	0.355	0.006	0.368
wrapper.mvPerLinesHistoPerCondition_HC	0.273	0.004	0.286
wrapper.mvPerLinesHisto_HC	0.273	0.006	0.287
wrapper.mvTypePlot	1.448	0.023	1.492
wrapper.normalizeD	0.279	0.003	0.290
wrapper.normalizeD2	0.345	0.004	0.360
wrapper.violinPlotD	1.680	0.019	1.726
wrapperCalibrationPlot	0.327	0.003	0.333
writeMSnsetToExcel	0.001	0.000	0.000