Package: DAPAR

Version: 1.18.5

Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:DAPAR.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings DAPAR_1.18.5.tar.gz

StartedAt: 2020-04-15 03:19:09 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 03:27:44 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 514.8 seconds

RetCode: 0

Status:  OK

CheckDir: DAPAR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:DAPAR.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings DAPAR_1.18.5.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/DAPAR.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.18.5’
* 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 ... NOTE
Package in Depends field not imported from: ‘igraph’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* 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’
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’
display.CC.visNet: no visible binding for global variable
  ‘layout_nicely’
getTextForGOAnalysis: no visible binding for global variable
  ‘textGOParams’
getTextForGOAnalysis: no visible binding for global variable ‘input’
Undefined global functions or variables:
  cond g input layout_nicely textGOParams x y
* checking Rd files ... NOTE
prepare_Rd: plotJitter_rCharts.Rd:20-23: Dropping empty section \examples
* 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 109.884 13.312 123.974
wrapper.dapar.impute.mi           11.908  0.364  12.295
compareNormalizationD_HC           8.084  0.980   9.065
buildGraph                         5.996  0.448   6.528
wrapper.CVDistD                    4.332  1.936   6.119
CVDistD                            4.088  1.832   5.840
wrapper.hc_mvTypePlot2             5.212  0.552   5.782
hc_mvTypePlot2                     5.164  0.580   5.813
CVDistD_HC                         4.000  1.248   5.674
display.CC.visNet                  4.168  0.368   5.091
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.10-bioc/meat/DAPAR.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL DAPAR
###
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* installing to library ‘/home/biocbuild/bbs-3.10-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 version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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
Loading required package: igraph

Attaching package: 'igraph'

The following object is masked from 'package:testthat':

    compare

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union


> 
> test_check("DAPAR")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 0 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 11.784   0.524  12.401 

name	user	system	elapsed
BuildAdjacencyMatrix	1.276	0.068	1.359
BuildColumnToProteinDataset	3.548	0.192	3.762
BuildColumnToProteinDataset_par	0	0	0
CVDistD	4.088	1.832	5.840
CVDistD_HC	4.000	1.248	5.674
CountPep	0.656	0.060	0.714
GetDetailedNbPeptides	1.120	0.020	1.143
Get_AllComparisons	0.584	0.016	0.620
GraphPepProt	0.412	0.008	0.421
NumericalFiltering	0.336	0.004	0.341
NumericalgetIndicesOfLinesToRemove	0.244	0.000	0.242
StringBasedFiltering	0.564	0.008	0.571
StringBasedFiltering2	0.288	0.012	0.300
addOriginOfValue	0.372	0.000	0.371
aggregateIter	3.700	0.124	3.825
aggregateIterParallel	2.976	1.172	2.524
aggregateMean	0.544	0.016	0.561
aggregateSum	0.924	0.104	1.030
aggregateTopn	2.484	0.056	2.547
boxPlotD	0.984	0.004	0.987
boxPlotD_HC	3.364	0.384	3.761
buildGraph	5.996	0.448	6.528
check.conditions	0.304	0.000	0.302
check.design	0.392	0.004	0.397
compareNormalizationD	0.652	0.004	0.655
compareNormalizationD_HC	8.084	0.980	9.065
compute.t.tests	1.244	0.172	1.412
corrMatrixD	0.616	0.028	0.646
corrMatrixD_HC	0.552	0.020	0.576
createMSnset	1.136	0.028	1.195
deleteLinesFromIndices	0.252	0.000	0.250
densityPlotD	0.232	0.000	0.232
densityPlotD_HC	3.816	0.536	4.410
diffAnaComputeFDR	0.332	0.000	0.331
diffAnaGetSignificant	0.652	0.008	0.658
diffAnaSave	0.472	0.036	0.507
diffAnaVolcanoplot	0.428	0.020	0.449
diffAnaVolcanoplot_rCharts	0	0	0
display.CC.visNet	4.168	0.368	5.091
enrich_GO	0	0	0
findMECBlock	0.532	0.068	0.597
formatLimmaResult	0.376	0.008	0.387
get.pep.prot.cc	1.328	0.008	1.339
getIndicesConditions	0.332	0.008	0.338
getIndicesOfLinesToRemove	0.236	0.004	0.242
getListNbValuesInLines	0.352	0.004	0.354
getNumberOf	0.232	0.000	0.234
getNumberOfEmptyLines	0.284	0.000	0.282
getPourcentageOfMV	0.412	0.004	0.417
getProcessingInfo	0.292	0.004	0.299
getProteinsStats	0.464	0.004	0.468
getQuantile4Imp	0.312	0.008	0.322
getTextForAggregation	0	0	0
getTextForAnaDiff	0.000	0.000	0.001
getTextForFiltering	0.000	0.000	0.001
getTextForGOAnalysis	0	0	0
getTextForHypothesisTest	0	0	0
getTextForNewDataset	0.000	0.000	0.003
getTextForNormalization	0.004	0.000	0.001
getTextForpeptideImputation	0.000	0.000	0.001
getTextForproteinImputation	0	0	0
group_GO	0	0	0
hc_logFC_DensityPlot	1.104	0.104	1.215
hc_mvTypePlot2	5.164	0.580	5.813
heatmap.DAPAR	0.572	0.004	0.577
heatmapD	0	0	0
histPValue_HC	0.672	0.012	0.689
impute.detQuant	0.736	0.228	0.965
impute.pa2	0.340	0.076	0.412
is.MV	0.452	0.208	0.674
is.OfType	0.384	0.164	0.555
limmaCompleteTest	0.312	0.000	0.311
make.contrast	0.360	0.004	0.368
make.design.1	0.380	0.004	0.387
make.design.2	0.000	0.000	0.001
make.design.3	0.404	0.008	0.412
make.design	0.396	0.000	0.396
mvFilter	0.472	0.012	0.493
mvFilterFromIndices	0.432	0.004	0.446
mvFilterGetIndices	0.464	0.032	0.497
mvHisto	0.360	0.000	0.361
mvHisto_HC	0.348	0.008	0.364
mvImage	3.180	0.064	3.267
mvPerLinesHisto	0.344	0.004	0.349
mvPerLinesHistoPerCondition	0.320	0.000	0.319
mvPerLinesHistoPerCondition_HC	0.332	0.012	0.344
mvPerLinesHisto_HC	0.304	0.008	0.310
my_hc_ExportMenu	0.108	0.024	0.143
my_hc_chart	0.124	0.032	0.157
nonzero	0.020	0.000	0.022
plotJitter	1.172	0.000	1.183
plotPCA_Eigen	0.380	0.000	0.382
plotPCA_Eigen_hc	0.300	0.000	0.304
plotPCA_Ind	0.228	0.000	0.229
plotPCA_Var	0.296	0.000	0.303
proportionConRev_HC	0.048	0.012	0.059
rbindMSnset	0.372	0.000	0.374
reIntroduceMEC	0.548	0.016	0.572
removeLines	0.224	0.000	0.224
saveParameters	0.356	0.000	0.356
setMEC	0.532	0.008	0.541
test.design	0.380	0.004	0.383
translatedRandomBeta	0.000	0.004	0.005
violinPlotD	1.144	0.024	1.206
wrapper.CVDistD	4.332	1.936	6.119
wrapper.CVDistD_HC	3.760	1.232	4.909
wrapper.compareNormalizationD	0.548	0.012	0.560
wrapper.compareNormalizationD_HC	109.884	13.312	123.974
wrapper.corrMatrixD	0.820	0.004	0.823
wrapper.corrMatrixD_HC	0.392	0.020	0.413
wrapper.dapar.impute.mi	11.908	0.364	12.295
wrapper.hc_mvTypePlot2	5.212	0.552	5.782
wrapper.heatmapD	0.004	0.000	0.000
wrapper.impute.KNN	0.444	0.004	0.447
wrapper.impute.detQuant	0.400	0.004	0.404
wrapper.impute.fixedValue	0.428	0.000	0.428
wrapper.impute.mle	0.472	0.004	0.476
wrapper.impute.pa	0.500	0.084	0.571
wrapper.impute.pa2	0.540	0.064	0.598
wrapper.impute.slsa	2.368	0.084	2.491
wrapper.mvHisto	0.396	0.000	0.398
wrapper.mvHisto_HC	0.388	0.008	0.396
wrapper.mvImage	0.712	0.008	0.719
wrapper.mvPerLinesHisto	0.348	0.004	0.352
wrapper.mvPerLinesHistoPerCondition	0.308	0.000	0.309
wrapper.mvPerLinesHistoPerCondition_HC	0.444	0.016	0.460
wrapper.mvPerLinesHisto_HC	0.408	0.000	0.410
wrapper.normalizeD	0.424	0.004	0.426
wrapper.pca	0.504	0.028	0.533
wrapper.t_test_Complete	0.456	0.008	0.464
wrapperCalibrationPlot	0.324	0.008	0.333
writeMSnsetToCSV	0	0	0
writeMSnsetToExcel	0	0	0