Multiple platform build/check report for BioC 3.9 - CHECK report for DAPAR on merida2

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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_1.15.12.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/DAPAR.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* 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 ‘1.15.12’
* 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 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 58.118  5.032  62.716
wrapper.dapar.impute.mi          12.988  0.862  13.848
CVDistD                           8.851  1.002   9.784
wrapper.CVDistD                   8.424  0.768   9.127
aggregateIterParallel             4.873  2.331   4.276
CVDistD_HC                        5.177  0.512   5.676
wrapper.CVDistD_HC                5.099  0.494   5.560
* 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’ ...
** 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
* DONE (DAPAR)

Tests output


R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
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)
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 
 12.423   0.844  13.353

Example timings

name	user	system	elapsed
BuildAdjacencyMatrix	1.284	0.202	1.488
BuildColumnToProteinDataset	1.038	0.066	1.102
BuildColumnToProteinDataset_par	2.331	1.807	1.246
CVDistD	8.851	1.002	9.784
CVDistD_HC	5.177	0.512	5.676
CountPep	0.554	0.162	0.713
GraphPepProt	0.453	0.051	0.504
StringBasedFiltering	0.607	0.050	0.659
StringBasedFiltering2	0.871	0.022	0.899
addOriginOfValue	0.281	0.007	0.290
aggregateIter	4.260	0.375	4.676
aggregateIterParallel	4.873	2.331	4.276
aggregateMean	0.431	0.046	0.483
aggregateSum	0.414	0.020	0.439
aggregateTopn	2.466	0.215	2.680
boxPlotD	0.366	0.012	0.382
boxPlotD_HC	2.137	0.240	2.380
check.conditions	0.342	0.005	0.350
check.design	0.278	0.006	0.285
compareNormalizationD	0.563	0.035	0.605
compareNormalizationD_HC	4.571	0.402	4.947
compute.t.tests	0.837	0.051	0.887
corrMatrixD	0.826	0.037	0.870
corrMatrixD_HC	0.442	0.059	0.509
createMSnset	0.904	0.083	0.987
deleteLinesFromIndices	0.504	0.024	0.531
densityPlotD	0.358	0.008	0.370
densityPlotD_HC	3.014	0.335	3.337
diffAnaComputeFDR	0.422	0.013	0.439
diffAnaGetSignificant	0.715	0.039	0.757
diffAnaSave	0.650	0.033	0.685
diffAnaVolcanoplot	0.362	0.011	0.377
diffAnaVolcanoplot_rCharts	0	0	0
enrich_GO	0.000	0.000	0.001
finalizeAggregation	0.459	0.016	0.477
findMECBlock	0.375	0.010	0.386
formatLimmaResult	0.446	0.017	0.465
getIndicesConditions	0.354	0.016	0.374
getIndicesOfLinesToRemove	0.308	0.004	0.313
getListNbValuesInLines	0.386	0.011	0.403
getNumberOf	0.301	0.004	0.308
getNumberOfEmptyLines	0.333	0.010	0.345
getPourcentageOfMV	0.325	0.008	0.339
getProcessingInfo	0.339	0.004	0.345
getProteinsStats	0.417	0.024	0.441
getQuantile4Imp	0.351	0.007	0.361
getTextForAggregation	0.000	0.000	0.001
getTextForAnaDiff	0.001	0.001	0.001
getTextForFiltering	0	0	0
getTextForGOAnalysis	0.001	0.000	0.000
getTextForHypothesisTest	0	0	0
getTextForNewDataset	0.003	0.001	0.004
getTextForNormalization	0	0	0
getTextForpeptideImputation	0	0	0
getTextForproteinImputation	0.000	0.000	0.001
group_GO	0.001	0.000	0.001
hc_logFC_DensityPlot	0.803	0.083	0.894
hc_mvTypePlot2	3.816	0.293	4.090
heatmap.DAPAR	0.546	0.026	0.575
heatmapD	0	0	0
heatmap_HC	1.018	0.104	1.119
histPValue_HC	0.585	0.057	0.655
impute.detQuant	0.854	0.510	1.424
impute.pa2	0.591	0.035	0.625
is.MV	0.848	0.554	1.412
is.OfType	0.827	0.544	1.365
limmaCompleteTest	0.428	0.016	0.447
make.contrast	0.298	0.005	0.304
make.design.1	0.330	0.007	0.340
make.design.2	0	0	0
make.design.3	0	0	0
make.design	0.322	0.005	0.328
mvFilter	0.418	0.015	0.441
mvFilterFromIndices	0.295	0.009	0.304
mvFilterGetIndices	0.502	0.124	0.624
mvHisto	0.304	0.005	0.313
mvHisto_HC	0.408	0.044	0.458
mvImage	4.215	0.276	4.478
mvPerLinesHisto	0.402	0.012	0.422
mvPerLinesHistoPerCondition	0.311	0.007	0.321
mvPerLinesHistoPerCondition_HC	0.404	0.046	0.452
mvPerLinesHisto_HC	0.371	0.041	0.416
my_hc_ExportMenu	0.173	0.117	0.300
my_hc_chart	0.168	0.119	0.302
nonzero	0.021	0.001	0.022
plotPCA_Eigen	0.287	0.005	0.295
plotPCA_Eigen_hc	0.341	0.004	0.348
plotPCA_Ind	0.291	0.003	0.295
plotPCA_Var	0.293	0.004	0.298
proportionConRev_HC	0.056	0.039	0.093
rbindMSnset	0.370	0.026	0.396
reIntroduceMEC	0.514	0.022	0.536
removeLines	0.373	0.010	0.386
rep_col	0.001	0.000	0.001
rep_row	0	0	0
saveParameters	0.276	0.007	0.285
setMEC	0.474	0.021	0.495
test.design	0.352	0.008	0.363
translatedRandomBeta	0.004	0.005	0.010
violinPlotD	0.892	0.023	0.918
wrapper.CVDistD	8.424	0.768	9.127
wrapper.CVDistD_HC	5.099	0.494	5.560
wrapper.compareNormalizationD	0.536	0.029	0.578
wrapper.compareNormalizationD_HC	58.118	5.032	62.716
wrapper.corrMatrixD	0.787	0.032	0.820
wrapper.corrMatrixD_HC	0.448	0.048	0.502
wrapper.dapar.impute.mi	12.988	0.862	13.848
wrapper.hc_mvTypePlot2	3.444	0.293	3.722
wrapper.heatmapD	0	0	0
wrapper.impute.KNN	0.349	0.008	0.357
wrapper.impute.detQuant	0.827	0.016	0.852
wrapper.impute.fixedValue	0.309	0.007	0.318
wrapper.impute.mle	0.386	0.011	0.398
wrapper.impute.pa	0.545	0.033	0.575
wrapper.impute.pa2	0.585	0.032	0.621
wrapper.impute.slsa	2.807	0.133	2.930
wrapper.mvHisto	0.301	0.005	0.310
wrapper.mvHisto_HC	0.373	0.045	0.421
wrapper.mvImage	0.790	0.039	0.834
wrapper.mvPerLinesHisto	0.402	0.006	0.424
wrapper.mvPerLinesHistoPerCondition	0.440	0.008	0.457
wrapper.mvPerLinesHistoPerCondition_HC	0.417	0.049	0.488
wrapper.mvPerLinesHisto_HC	0.335	0.005	0.343
wrapper.normalizeD	0.325	0.008	0.337
wrapper.pca	0.318	0.005	0.325
wrapper.t_test_Complete	0.538	0.021	0.559
wrapperCalibrationPlot	0.367	0.011	0.379
writeMSnsetToCSV	0	0	0
writeMSnsetToExcel	0.000	0.000	0.001

CHECK report for DAPAR on merida2

Summary

Command output

Installation output

Tests output

Example timings