Multiple platform build/check report for BioC 3.11 - CHECK report for DAPAR on celaya2

Package: DAPAR

Version: 1.19.13

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:DAPAR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings DAPAR_1.19.13.tar.gz

StartedAt: 2020-01-16 03:29:10 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 03:43:29 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 858.4 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 --install=check:DAPAR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings DAPAR_1.19.13.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/DAPAR.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘1.19.13’
* checking package namespace information ... NOTE
  Namespace with empty importFrom: ‘preprocessCore’
* 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
Namespace in Imports field not imported from: ‘igraph’
  All declared Imports should be used.
* 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’
compute.t.tests2: no visible binding for global variable ‘Cond.Nb’
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’
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’
groupttest: no visible binding for global variable ‘qData’
groupttest: no visible binding for global variable ‘c1Indice’
groupttest: no visible binding for global variable ‘c2Indice’
Undefined global functions or variables:
  Cond.Nb c1Indice c2Indice cond conds g input layout_nicely qData
  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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                   user system elapsed
wrapper.compareNormalizationD_HC 79.260 53.112 130.180
CVDistD                          12.060 11.286  22.963
wrapper.CVDistD                  11.926 11.256  22.787
wrapper.dapar.impute.mi          17.195  2.486  21.833
CVDistD_HC                        7.397  6.434  13.655
wrapper.CVDistD_HC                7.261  6.359  13.394
buildGraph                        8.254  2.376  10.624
groupttest                        7.627  2.354   9.950
compareNormalizationD_HC          6.028  3.875   9.772
compute.group.t.tests             6.858  2.358   9.181
display.CC.visNet                 6.214  1.936   8.147
hc_mvTypePlot2                    4.550  2.274   6.745
wrapper.hc_mvTypePlot2            4.349  2.094   6.376
mvImage                           5.657  0.563   6.208
aggregateIter                     5.296  0.627   5.920
aggregateIterParallel             4.242  1.590   3.777
densityPlotD_HC                   3.327  2.065   5.327
BuildColumnToProteinDataset       4.490  0.785   5.268
* 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/DAPAR.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL DAPAR
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/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) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 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)
Loading required package: foreach
Loading required package: parallel
Loading required package: doParallel
Loading required package: iterators

> 
> test_check("DAPAR")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 0 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 20.483   2.712  23.118

name	user	system	elapsed
BuildAdjacencyMatrix	1.754	0.378	2.169
BuildColumnToProteinDataset	4.490	0.785	5.268
BuildColumnToProteinDataset_par	0	0	0
CVDistD	12.060	11.286	22.963
CVDistD_HC	7.397	6.434	13.655
CountPep	0.805	0.318	1.121
GetDetailedNbPeptides	0.668	0.106	0.773
GraphPepProt	0.643	0.050	0.693
NumericalFiltering	0.621	0.053	0.673
NumericalgetIndicesOfLinesToRemove	0.414	0.012	0.426
StringBasedFiltering	0.868	0.111	0.978
StringBasedFiltering2	1.200	0.057	1.257
addOriginOfValue	0.351	0.019	0.369
aggregateIter	5.296	0.627	5.920
aggregateIterParallel	4.242	1.590	3.777
aggregateMean	0.797	0.085	0.879
aggregateSum	0.917	0.082	0.999
aggregateTopn	3.553	0.495	4.036
boxPlotD	0.504	0.033	0.538
boxPlotD_HC	3.176	1.797	4.934
buildGraph	8.254	2.376	10.624
check.conditions	0.380	0.008	0.387
check.design	0.393	0.010	0.404
compareNormalizationD	0.573	0.048	0.627
compareNormalizationDSubset	0.414	0.038	0.476
compareNormalizationD_HC	6.028	3.875	9.772
compute.group.t.tests	6.858	2.358	9.181
compute.t.tests	2.375	0.673	3.021
compute.t.tests2	2.336	0.666	2.975
corrMatrixD	0.793	0.083	0.879
corrMatrixD_HC	0.435	0.145	0.578
createMSnset	1.505	0.171	1.673
deleteLinesFromIndices	0.447	0.024	0.471
densityPlotD	0.367	0.014	0.381
densityPlotD_HC	3.327	2.065	5.327
diffAnaComputeFDR	0.556	0.030	0.585
diffAnaGetSignificant	0.850	0.081	0.927
diffAnaSave	0.797	0.078	0.872
diffAnaVolcanoplot	0.481	0.033	0.514
diffAnaVolcanoplot_rCharts	0.001	0.000	0.000
display.CC.visNet	6.214	1.936	8.147
enrich_GO	0.000	0.001	0.001
findMECBlock	0.407	0.021	0.427
formatLimmaResult	0.533	0.040	0.570
get.pep.prot.cc	1.449	0.101	1.548
getIndicesConditions	0.274	0.008	0.281
getIndicesOfLinesToRemove	0.373	0.009	0.382
getListNbValuesInLines	0.459	0.022	0.480
getNumberOf	0.361	0.008	0.369
getNumberOfEmptyLines	0.369	0.021	0.390
getPourcentageOfMV	0.405	0.017	0.422
getProcessingInfo	0.306	0.008	0.313
getProteinsStats	0.474	0.050	0.523
getQuantile4Imp	0.350	0.013	0.362
getTextForAggregation	0.000	0.000	0.001
getTextForAnaDiff	0.001	0.000	0.002
getTextForFiltering	0.001	0.001	0.001
getTextForGOAnalysis	0.000	0.000	0.001
getTextForHypothesisTest	0.000	0.000	0.001
getTextForNewDataset	0.003	0.001	0.005
getTextForNormalization	0.001	0.000	0.001
getTextForpeptideImputation	0.001	0.001	0.001
getTextForproteinImputation	0.001	0.000	0.001
group_GO	0.001	0.000	0.000
groupttest	7.627	2.354	9.950
hc_logFC_DensityPlot	1.033	0.499	1.520
hc_mvTypePlot2	4.550	2.274	6.745
heatmap.DAPAR	0.701	0.053	0.758
heatmapD	0.001	0.001	0.001
histPValue_HC	0.733	0.151	0.900
impute.detQuant	1.174	1.000	2.668
impute.pa2	0.777	0.416	1.178
is.MV	1.250	1.100	2.356
is.OfType	1.102	1.075	2.186
limmaCompleteTest	0.575	0.050	0.624
make.contrast	0.351	0.011	0.362
make.design.1	0.292	0.009	0.301
make.design.2	0.000	0.001	0.001
make.design.3	0.001	0.000	0.000
make.design	0.381	0.009	0.389
mvFilter	0.470	0.030	0.498
mvFilterFromIndices	0.355	0.019	0.373
mvFilterGetIndices	0.643	0.230	0.871
mvHisto	0.332	0.011	0.343
mvHisto_HC	0.468	0.097	0.570
mvImage	5.657	0.563	6.208
mvPerLinesHisto	0.487	0.020	0.521
mvPerLinesHistoPerCondition	0.434	0.013	0.447
mvPerLinesHistoPerCondition_HC	0.502	0.100	0.608
mvPerLinesHisto_HC	0.523	0.106	0.642
my_hc_ExportMenu	0.250	0.250	0.566
my_hc_chart	0.247	0.244	0.510
nonzero	0.041	0.003	0.044
plotJitter	1.603	0.114	1.715
plotPCA_Eigen	0.385	0.009	0.393
plotPCA_Eigen_hc	0.392	0.010	0.402
plotPCA_Ind	0.403	0.011	0.415
plotPCA_Var	0.352	0.010	0.360
proportionConRev_HC	0.095	0.091	0.188
rbindMSnset	0.411	0.042	0.454
reIntroduceMEC	0.617	0.047	0.663
removeLines	0.314	0.015	0.328
saveParameters	0.272	0.010	0.283
setMEC	0.543	0.042	0.584
splitAdjacencyMat	0.517	0.137	0.649
test.design	0.380	0.009	0.390
translatedRandomBeta	0.008	0.010	0.017
violinPlotD	1.235	0.082	1.321
wrapper.CVDistD	11.926	11.256	22.787
wrapper.CVDistD_HC	7.261	6.359	13.394
wrapper.compareNormalizationD	0.642	0.055	0.701
wrapper.compareNormalizationDSubset	0.454	0.032	0.493
wrapper.compareNormalizationD_HC	79.260	53.112	130.180
wrapper.corrMatrixD	0.853	0.125	0.974
wrapper.corrMatrixD_HC	0.534	0.151	0.696
wrapper.dapar.impute.mi	17.195	2.486	21.833
wrapper.hc_mvTypePlot2	4.349	2.094	6.376
wrapper.heatmapD	0.001	0.000	0.001
wrapper.impute.KNN	0.434	0.022	0.456
wrapper.impute.detQuant	0.365	0.018	0.384
wrapper.impute.fixedValue	0.387	0.020	0.408
wrapper.impute.mle	0.489	0.029	0.518
wrapper.impute.pa	0.781	0.385	1.154
wrapper.impute.pa2	0.750	0.423	1.163
wrapper.impute.slsa	3.425	0.393	3.805
wrapper.mvHisto	0.386	0.010	0.397
wrapper.mvHisto_HC	0.476	0.097	0.586
wrapper.mvImage	0.978	0.086	1.069
wrapper.mvPerLinesHisto	0.420	0.012	0.433
wrapper.mvPerLinesHistoPerCondition	0.426	0.016	0.442
wrapper.mvPerLinesHistoPerCondition_HC	0.615	0.129	0.746
wrapper.mvPerLinesHisto_HC	0.383	0.011	0.394
wrapper.normalizeD	0.369	0.018	0.388
wrapper.pca	0.387	0.009	0.396
wrapper.t_test_Complete	0.427	0.026	0.452
wrapperCalibrationPlot	0.529	0.034	0.561
writeMSnsetToCSV	0.000	0.000	0.001
writeMSnsetToExcel	0	0	0

CHECK report for DAPAR on celaya2

Summary

Command output

Installation output

Tests output

Example timings