Multiple platform build/check report for BioC 3.9 - CHECK report for DAPAR on celaya2

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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_1.16.11.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/DAPAR.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.16.11’
* 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
  ‘swap’
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 swap 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                                   user system elapsed
wrapper.compareNormalizationD_HC 75.623 51.025 125.023
CVDistD                          12.253 11.625  23.577
wrapper.CVDistD                  11.166 11.026  21.899
wrapper.dapar.impute.mi          16.776  2.176  18.901
wrapper.CVDistD_HC                6.946  6.312  13.087
CVDistD_HC                        6.741  6.258  12.869
aggregateIterParallel             5.684  4.716   5.599
compareNormalizationD_HC          5.226  3.703   8.786
BuildColumnToProteinDataset_par   3.670  4.098   2.234
hc_mvTypePlot2                    3.994  2.147   6.088
wrapper.hc_mvTypePlot2            4.094  1.884   6.181
mvImage                           5.240  0.543   5.769
aggregateIter                     4.866  0.646   5.509
* 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
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/DAPAR.Rcheck/00check.log’
for details.

Installation output

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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/3.6/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)

Tests output


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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: 3 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 16.631   2.189  18.755

Example timings

name	user	system	elapsed
BuildAdjacencyMatrix	1.51	0.34	1.85
BuildColumnToProteinDataset	1.325	0.158	1.480
BuildColumnToProteinDataset_par	3.670	4.098	2.234
CVDistD	12.253	11.625	23.577
CVDistD_HC	6.741	6.258	12.869
CountPep	0.721	0.329	1.048
GraphPepProt	0.606	0.081	0.686
StringBasedFiltering	0.832	0.137	0.966
StringBasedFiltering2	0.529	0.048	0.577
addOriginOfValue	0.394	0.032	0.427
aggregateIter	4.866	0.646	5.509
aggregateIterParallel	5.684	4.716	5.599
aggregateMean	0.609	0.104	0.713
aggregateSum	0.649	0.087	0.735
aggregateTopn	3.845	0.667	4.504
boxPlotD	0.424	0.027	0.450
boxPlotD_HC	2.503	1.501	3.965
check.conditions	0.363	0.013	0.375
check.design	0.302	0.010	0.313
compareNormalizationD	0.527	0.050	0.579
compareNormalizationD_HC	5.226	3.703	8.786
compute.t.tests	2.216	0.653	2.847
corrMatrixD	0.944	0.096	1.048
corrMatrixD_HC	0.489	0.149	0.637
createMSnset	1.139	0.201	1.340
deleteLinesFromIndices	0.681	0.062	0.742
densityPlotD	0.310	0.023	0.333
densityPlotD_HC	2.903	1.929	4.785
diffAnaComputeFDR	0.509	0.030	0.549
diffAnaGetSignificant	0.891	0.088	0.976
diffAnaSave	0.771	0.081	0.850
diffAnaVolcanoplot	0.475	0.029	0.503
diffAnaVolcanoplot_rCharts	0.000	0.000	0.001
enrich_GO	0.001	0.000	0.001
finalizeAggregation	0.613	0.058	0.670
findMECBlock	1.018	0.318	1.328
formatLimmaResult	0.562	0.041	0.602
getIndicesConditions	0.36	0.01	0.37
getIndicesOfLinesToRemove	0.366	0.015	0.381
getListNbValuesInLines	0.517	0.037	0.554
getNumberOf	0.396	0.009	0.405
getNumberOfEmptyLines	0.371	0.019	0.389
getPourcentageOfMV	0.406	0.019	0.425
getProcessingInfo	0.288	0.010	0.299
getProteinsStats	0.546	0.057	0.602
getQuantile4Imp	0.378	0.011	0.390
getTextForAggregation	0.001	0.001	0.001
getTextForAnaDiff	0.001	0.001	0.002
getTextForFiltering	0.001	0.000	0.002
getTextForGOAnalysis	0.001	0.000	0.001
getTextForHypothesisTest	0.000	0.000	0.001
getTextForNewDataset	0.004	0.001	0.005
getTextForNormalization	0.001	0.001	0.001
getTextForpeptideImputation	0.000	0.000	0.001
getTextForproteinImputation	0.000	0.000	0.001
group_GO	0	0	0
hc_logFC_DensityPlot	1.040	0.434	1.465
hc_mvTypePlot2	3.994	2.147	6.088
heatmap.DAPAR	0.682	0.050	0.732
heatmapD	0.000	0.000	0.001
heatmap_HC	1.353	0.673	2.012
histPValue_HC	0.751	0.135	0.894
impute.detQuant	1.344	0.997	2.340
impute.pa2	0.739	0.417	1.144
is.MV	1.284	1.105	2.384
is.OfType	1.141	1.073	2.209
limmaCompleteTest	0.608	0.037	0.645
make.contrast	0.357	0.011	0.368
make.design.1	0.392	0.012	0.403
make.design.2	0	0	0
make.design.3	0	0	0
make.design	1.143	0.025	1.168
mvFilter	0.444	0.038	0.481
mvFilterFromIndices	0.389	0.018	0.406
mvFilterGetIndices	0.482	0.226	0.707
mvHisto	0.366	0.010	0.376
mvHisto_HC	0.422	0.100	0.521
mvImage	5.240	0.543	5.769
mvPerLinesHisto	0.385	0.020	0.412
mvPerLinesHistoPerCondition	0.379	0.011	0.390
mvPerLinesHistoPerCondition_HC	0.435	0.105	0.540
mvPerLinesHisto_HC	0.475	0.096	0.571
my_hc_ExportMenu	0.235	0.233	0.468
my_hc_chart	0.239	0.256	0.500
nonzero	0.032	0.003	0.035
plotPCA_Eigen	0.390	0.008	0.399
plotPCA_Eigen_hc	0.369	0.011	0.380
plotPCA_Ind	0.271	0.010	0.282
plotPCA_Var	0.382	0.012	0.396
proportionConRev_HC	0.093	0.090	0.183
rbindMSnset	0.458	0.041	0.500
reIntroduceMEC	0.659	0.043	0.700
removeLines	0.321	0.017	0.339
rep_col	0.001	0.000	0.001
rep_row	0.000	0.001	0.001
saveParameters	0.335	0.020	0.355
setMEC	0.564	0.054	0.615
test.design	0.388	0.011	0.399
translatedRandomBeta	0.009	0.013	0.022
violinPlotD	1.198	0.066	1.269
wrapper.CVDistD	11.166	11.026	21.899
wrapper.CVDistD_HC	6.946	6.312	13.087
wrapper.compareNormalizationD	0.546	0.043	0.590
wrapper.compareNormalizationD_HC	75.623	51.025	125.023
wrapper.corrMatrixD	0.892	0.127	1.015
wrapper.corrMatrixD_HC	0.527	0.140	0.664
wrapper.dapar.impute.mi	16.776	2.176	18.901
wrapper.hc_mvTypePlot2	4.094	1.884	6.181
wrapper.heatmapD	0.000	0.000	0.001
wrapper.impute.KNN	0.452	0.015	0.724
wrapper.impute.detQuant	0.484	0.018	0.759
wrapper.impute.fixedValue	0.423	0.014	0.671
wrapper.impute.mle	0.572	0.031	0.978
wrapper.impute.pa	0.734	0.250	1.278
wrapper.impute.pa2	1.495	0.354	2.049
wrapper.impute.slsa	3.289	0.376	3.654
wrapper.mvHisto	0.387	0.010	0.397
wrapper.mvHisto_HC	0.491	0.098	0.589
wrapper.mvImage	0.936	0.086	1.020
wrapper.mvPerLinesHisto	0.469	0.017	0.487
wrapper.mvPerLinesHistoPerCondition	0.293	0.011	0.305
wrapper.mvPerLinesHistoPerCondition_HC	0.472	0.101	0.570
wrapper.mvPerLinesHisto_HC	0.350	0.012	0.365
wrapper.normalizeD	0.435	0.019	0.454
wrapper.pca	0.373	0.011	0.384
wrapper.t_test_Complete	0.330	0.024	0.354
wrapperCalibrationPlot	0.540	0.032	0.571
writeMSnsetToCSV	0.000	0.000	0.001
writeMSnsetToExcel	0.000	0.000	0.001

CHECK report for DAPAR on celaya2

Summary

Command output

Installation output

Tests output

Example timings