Package: DAPAR

Version: 1.15.12

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:DAPAR.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings DAPAR_1.15.12.tar.gz

StartedAt: 2019-04-08 23:51:25 -0400 (Mon, 08 Apr 2019)

EndedAt: 2019-04-08 23:57:58 -0400 (Mon, 08 Apr 2019)

EllapsedTime: 392.7 seconds

RetCode: 0

Status:  OK

CheckDir: DAPAR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:DAPAR.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings DAPAR_1.15.12.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/DAPAR.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.15.12’
* 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 ... NOTE
boxPlotD: warning in axis(side = 1, at = 1:ncol(qData), label =
  legend): partial argument match of 'label' to 'labels'
heatmap.DAPAR: warning in axis(1, 1:nc, label = labCol, las = 2, line =
  -0.5 + offsetCol, tick = 0, cex.axis = cexCol, hadj = NA, padj = 0):
  partial argument match of 'label' to 'labels'
heatmap.DAPAR: warning in axis(1, 1:nc, label = rep("", nc), las = 2,
  tick = 0): partial argument match of 'label' to 'labels'
heatmap.DAPAR: warning in axis(4, iy, label = labRow, las = 5, line =
  -0.5 + offsetRow, tick = 0, cex.axis = cexRow, hadj = 0, padj = NA):
  partial argument match of 'label' to 'labels'
heatmap.DAPAR: warning in axis(4, iy, label = rep("", nr), las = 2,
  line = -0.5, tick = 0): partial argument match of 'label' to 'labels'
violinPlotD: warning in axis(side = 1, at = 1:ncol(qData), label = if
  (is.vector(legend)) {: partial argument match of 'label' to 'labels'
violinPlotD: warning in legend: partial argument match of 'label' to
  'labels'
violinPlotD: warning in } else {: partial argument match of 'label' to
  'labels'
violinPlotD: warning in legend[, i]: partial argument match of 'label'
  to 'labels'
violinPlotD: warning in }, line = 2 * i - 1): partial argument match of
  'label' to 'labels'
aggregateIterParallel: no visible binding for global variable ‘cond’
boxPlotD: no visible binding for global variable ‘conds’
densityPlotD: no visible binding for global variable ‘conds’
diffAnaVolcanoplot_rCharts: no visible binding for global variable ‘x’
diffAnaVolcanoplot_rCharts: no visible binding for global variable ‘y’
diffAnaVolcanoplot_rCharts: no visible binding for global variable ‘g’
getTextForGOAnalysis: no visible binding for global variable
  ‘textGOParams’
getTextForGOAnalysis: no visible binding for global variable ‘input’
heatmap_HC: no visible binding for global variable ‘Exp1_R25_pept’
heatmap_HC: no visible binding for global variable ‘condition’
heatmap_HC: no visible binding for global variable ‘id’
heatmap_HC: no visible binding for global variable ‘value’
Undefined global functions or variables:
  Exp1_R25_pept cond condition conds g id input textGOParams value x y
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                                   user system elapsed
wrapper.compareNormalizationD_HC 36.297  9.468  50.263
wrapper.dapar.impute.mi          14.063  0.312  14.498
wrapper.CVDistD                   4.478  2.017   6.752
CVDistD                           4.036  1.911   6.958
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/DAPAR.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL DAPAR
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘DAPAR’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (DAPAR)

R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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)
Loading required package: foreach
Loading required package: parallel
Loading required package: doParallel
Loading required package: iterators

> 
> test_check("DAPAR")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 3 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  9.899   0.413  10.272 

name	user	system	elapsed
BuildAdjacencyMatrix	1.312	0.108	1.832
BuildColumnToProteinDataset	1.071	0.043	1.169
BuildColumnToProteinDataset_par	2.191	1.001	1.863
CVDistD	4.036	1.911	6.958
CVDistD_HC	2.840	1.076	4.639
CountPep	1.083	0.123	1.212
GraphPepProt	0.486	0.015	0.525
StringBasedFiltering	0.659	0.017	0.718
StringBasedFiltering2	0.538	0.008	0.548
addOriginOfValue	0.396	0.000	0.396
aggregateIter	4.084	0.191	4.303
aggregateIterParallel	2.661	0.442	2.090
aggregateMean	0.487	0.036	0.525
aggregateSum	0.462	0.010	0.475
aggregateTopn	2.069	0.097	2.195
boxPlotD	0.480	0.003	0.492
boxPlotD_HC	1.520	0.301	1.945
check.conditions	0.417	0.003	0.427
check.design	0.400	0.000	0.405
compareNormalizationD	0.657	0.017	0.677
compareNormalizationD_HC	2.708	0.630	3.288
compute.t.tests	0.892	0.053	0.930
corrMatrixD	0.854	0.024	0.878
corrMatrixD_HC	0.503	0.032	0.533
createMSnset	0.840	0.040	0.968
deleteLinesFromIndices	0.485	0.011	0.499
densityPlotD	0.421	0.000	0.425
densityPlotD_HC	1.658	0.363	2.246
diffAnaComputeFDR	0.478	0.007	0.490
diffAnaGetSignificant	0.701	0.016	0.729
diffAnaSave	0.747	0.023	0.772
diffAnaVolcanoplot	0.49	0.02	0.51
diffAnaVolcanoplot_rCharts	0	0	0
enrich_GO	0.001	0.000	0.000
finalizeAggregation	0.467	0.007	0.475
findMECBlock	0.418	0.000	0.419
formatLimmaResult	0.544	0.008	0.600
getIndicesConditions	0.393	0.000	0.393
getIndicesOfLinesToRemove	0.390	0.000	0.391
getListNbValuesInLines	0.502	0.000	0.504
getNumberOf	0.370	0.000	0.375
getNumberOfEmptyLines	0.436	0.004	0.469
getPourcentageOfMV	0.388	0.003	0.395
getProcessingInfo	0.372	0.004	0.386
getProteinsStats	0.448	0.008	0.456
getQuantile4Imp	0.399	0.000	0.399
getTextForAggregation	0.001	0.000	0.000
getTextForAnaDiff	0.001	0.000	0.001
getTextForFiltering	0.001	0.000	0.001
getTextForGOAnalysis	0.001	0.000	0.001
getTextForHypothesisTest	0.001	0.000	0.001
getTextForNewDataset	0.002	0.000	0.003
getTextForNormalization	0.001	0.000	0.000
getTextForpeptideImputation	0.001	0.000	0.001
getTextForproteinImputation	0	0	0
group_GO	0	0	0
hc_logFC_DensityPlot	0.689	0.069	0.746
hc_mvTypePlot2	1.940	0.391	2.340
heatmap.DAPAR	0.775	0.012	0.786
heatmapD	0	0	0
heatmap_HC	0.911	0.125	1.159
histPValue_HC	0.650	0.025	0.684
impute.detQuant	0.709	0.204	0.917
impute.pa2	0.510	0.048	0.576
is.MV	0.649	0.223	0.924
is.OfType	0.642	0.232	0.915
limmaCompleteTest	0.541	0.000	0.552
make.contrast	0.380	0.004	0.384
make.design.1	0.386	0.000	0.391
make.design.2	0	0	0
make.design.3	0	0	0
make.design	0.391	0.000	0.395
mvFilter	0.504	0.003	0.511
mvFilterFromIndices	0.395	0.007	0.411
mvFilterGetIndices	0.488	0.044	0.540
mvHisto	0.396	0.000	0.397
mvHisto_HC	0.426	0.027	0.453
mvImage	3.680	0.160	3.972
mvPerLinesHisto	0.482	0.010	0.503
mvPerLinesHistoPerCondition	0.404	0.002	0.409
mvPerLinesHistoPerCondition_HC	0.510	0.012	0.545
mvPerLinesHisto_HC	0.450	0.016	0.469
my_hc_ExportMenu	0.132	0.035	0.179
my_hc_chart	0.135	0.032	0.183
nonzero	0.020	0.000	0.021
plotPCA_Eigen	0.396	0.004	0.400
plotPCA_Eigen_hc	0.384	0.008	0.396
plotPCA_Ind	0.424	0.004	0.430
plotPCA_Var	0.365	0.008	0.374
proportionConRev_HC	0.042	0.016	0.057
rbindMSnset	0.395	0.015	0.431
reIntroduceMEC	0.538	0.007	0.547
removeLines	0.437	0.004	0.441
rep_col	0	0	0
rep_row	0	0	0
saveParameters	0.407	0.000	0.408
setMEC	0.487	0.011	0.504
test.design	0.393	0.001	0.393
translatedRandomBeta	0.005	0.000	0.005
violinPlotD	1.065	0.007	1.070
wrapper.CVDistD	4.478	2.017	6.752
wrapper.CVDistD_HC	2.837	1.033	4.445
wrapper.compareNormalizationD	0.610	0.004	0.627
wrapper.compareNormalizationD_HC	36.297	9.468	50.263
wrapper.corrMatrixD	0.749	0.027	0.853
wrapper.corrMatrixD_HC	0.557	0.031	0.589
wrapper.dapar.impute.mi	14.063	0.312	14.498
wrapper.hc_mvTypePlot2	2.616	0.359	2.882
wrapper.heatmapD	0.001	0.000	0.001
wrapper.impute.KNN	0.269	0.007	0.276
wrapper.impute.detQuant	0.286	0.006	0.292
wrapper.impute.fixedValue	0.416	0.004	0.418
wrapper.impute.mle	0.358	0.004	0.362
wrapper.impute.pa	0.346	0.057	0.389
wrapper.impute.pa2	0.514	0.097	0.593
wrapper.impute.slsa	1.975	0.060	2.020
wrapper.mvHisto	0.225	0.003	0.228
wrapper.mvHisto_HC	0.266	0.008	0.273
wrapper.mvImage	1.331	0.007	1.335
wrapper.mvPerLinesHisto	0.378	0.000	0.378
wrapper.mvPerLinesHistoPerCondition	0.435	0.000	0.435
wrapper.mvPerLinesHistoPerCondition_HC	0.451	0.015	0.466
wrapper.mvPerLinesHisto_HC	0.242	0.000	0.241
wrapper.normalizeD	0.426	0.004	0.429
wrapper.pca	0.387	0.000	0.387
wrapper.t_test_Complete	0.611	0.008	0.617
wrapperCalibrationPlot	0.464	0.003	0.467
writeMSnsetToCSV	0	0	0
writeMSnsetToExcel	0	0	0