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_1.15.12.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/DAPAR.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 72.980 49.407 121.186
wrapper.CVDistD                  11.747 10.602  22.056
CVDistD                          11.118 10.762  21.614
wrapper.dapar.impute.mi          15.411  2.429  18.774
CVDistD_HC                        7.332  6.209  13.411
aggregateIterParallel             8.121  4.468   7.565
wrapper.CVDistD_HC                6.514  5.862  12.243
compareNormalizationD_HC          5.342  3.555   8.811
BuildColumnToProteinDataset_par   3.804  4.198   2.226
aggregateIter                     6.371  1.048   7.417
hc_mvTypePlot2                    4.118  2.016   6.077
mvImage                           5.304  0.511   5.798
wrapper.hc_mvTypePlot2            4.056  1.580   6.750
densityPlotD_HC                   3.124  1.911   4.997
* 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 Under development (unstable) (2019-03-18 r76245) -- "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: 3 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 15.687   2.022  17.647

Example timings

name	user	system	elapsed
BuildAdjacencyMatrix	1.530	0.389	1.916
BuildColumnToProteinDataset	1.431	0.154	1.582
BuildColumnToProteinDataset_par	3.804	4.198	2.226
CVDistD	11.118	10.762	21.614
CVDistD_HC	7.332	6.209	13.411
CountPep	0.612	0.325	0.935
GraphPepProt	0.588	0.123	0.706
StringBasedFiltering	0.790	0.125	0.914
StringBasedFiltering2	1.032	0.060	1.092
addOriginOfValue	0.390	0.016	0.406
aggregateIter	6.371	1.048	7.417
aggregateIterParallel	8.121	4.468	7.565
aggregateMean	0.458	0.087	0.545
aggregateSum	0.615	0.089	0.704
aggregateTopn	3.039	0.414	3.446
boxPlotD	0.318	0.024	0.342
boxPlotD_HC	2.652	1.575	4.178
check.conditions	0.394	0.012	0.406
check.design	0.260	0.010	0.269
compareNormalizationD	0.663	0.062	0.725
compareNormalizationD_HC	5.342	3.555	8.811
compute.t.tests	1.119	0.322	1.434
corrMatrixD	0.875	0.093	0.969
corrMatrixD_HC	0.500	0.143	0.641
createMSnset	1.193	0.188	1.382
deleteLinesFromIndices	0.408	0.045	0.453
densityPlotD	0.415	0.016	0.431
densityPlotD_HC	3.124	1.911	4.997
diffAnaComputeFDR	0.420	0.027	0.447
diffAnaGetSignificant	0.690	0.083	0.770
diffAnaSave	0.724	0.090	0.813
diffAnaVolcanoplot	0.330	0.027	0.358
diffAnaVolcanoplot_rCharts	0.001	0.001	0.001
enrich_GO	0	0	0
finalizeAggregation	0.374	0.035	0.408
findMECBlock	0.438	0.022	0.459
formatLimmaResult	0.583	0.044	0.627
getIndicesConditions	0.363	0.009	0.372
getIndicesOfLinesToRemove	0.379	0.013	0.391
getListNbValuesInLines	0.326	0.022	0.346
getNumberOf	0.33	0.01	0.34
getNumberOfEmptyLines	0.305	0.018	0.323
getPourcentageOfMV	0.475	0.020	0.496
getProcessingInfo	0.278	0.008	0.286
getProteinsStats	0.347	0.039	0.385
getQuantile4Imp	0.343	0.011	0.355
getTextForAggregation	0.000	0.000	0.001
getTextForAnaDiff	0.000	0.000	0.001
getTextForFiltering	0.000	0.001	0.001
getTextForGOAnalysis	0.000	0.000	0.001
getTextForHypothesisTest	0.001	0.000	0.001
getTextForNewDataset	0.005	0.003	0.009
getTextForNormalization	0.001	0.000	0.001
getTextForpeptideImputation	0.000	0.000	0.001
getTextForproteinImputation	0.001	0.000	0.001
group_GO	0.001	0.000	0.001
hc_logFC_DensityPlot	1.081	0.439	1.519
hc_mvTypePlot2	4.118	2.016	6.077
heatmap.DAPAR	0.650	0.048	0.700
heatmapD	0.000	0.000	0.001
heatmap_HC	1.241	0.629	1.846
histPValue_HC	0.708	0.125	0.834
impute.detQuant	1.272	0.966	2.232
impute.pa2	0.633	0.397	1.015
is.MV	1.047	0.992	2.033
is.OfType	1.060	1.027	2.084
limmaCompleteTest	0.514	0.034	0.547
make.contrast	0.447	0.033	0.481
make.design.1	0.397	0.011	0.408
make.design.2	0.000	0.000	0.001
make.design.3	0	0	0
make.design	0.355	0.010	0.366
mvFilter	0.381	0.028	0.408
mvFilterFromIndices	0.277	0.015	0.292
mvFilterGetIndices	0.556	0.244	0.799
mvHisto	0.414	0.019	0.434
mvHisto_HC	0.380	0.096	0.474
mvImage	5.304	0.511	5.798
mvPerLinesHisto	0.498	0.023	0.524
mvPerLinesHistoPerCondition	0.446	0.013	0.460
mvPerLinesHistoPerCondition_HC	0.521	0.117	0.637
mvPerLinesHisto_HC	0.438	0.111	0.550
my_hc_ExportMenu	0.238	0.240	0.504
my_hc_chart	0.222	0.239	0.464
nonzero	0.034	0.003	0.047
plotPCA_Eigen	0.437	0.018	0.455
plotPCA_Eigen_hc	0.321	0.008	0.329
plotPCA_Ind	0.389	0.010	0.398
plotPCA_Var	0.267	0.009	0.276
proportionConRev_HC	0.086	0.086	0.171
rbindMSnset	0.476	0.041	0.518
reIntroduceMEC	0.755	0.045	0.799
removeLines	0.477	0.018	0.495
rep_col	0.001	0.000	0.001
rep_row	0	0	0
saveParameters	0.334	0.024	0.358
setMEC	0.609	0.040	0.649
test.design	0.405	0.011	0.415
translatedRandomBeta	0.009	0.013	0.022
violinPlotD	1.199	0.057	1.255
wrapper.CVDistD	11.747	10.602	22.056
wrapper.CVDistD_HC	6.514	5.862	12.243
wrapper.compareNormalizationD	0.504	0.046	0.552
wrapper.compareNormalizationD_HC	72.980	49.407	121.186
wrapper.corrMatrixD	1.066	0.119	1.183
wrapper.corrMatrixD_HC	0.476	0.129	0.605
wrapper.dapar.impute.mi	15.411	2.429	18.774
wrapper.hc_mvTypePlot2	4.056	1.580	6.750
wrapper.heatmapD	0.001	0.001	0.001
wrapper.impute.KNN	0.368	0.020	0.388
wrapper.impute.detQuant	0.397	0.024	0.421
wrapper.impute.fixedValue	0.348	0.020	0.368
wrapper.impute.mle	0.472	0.025	0.499
wrapper.impute.pa	0.760	0.366	1.113
wrapper.impute.pa2	0.714	0.402	1.100
wrapper.impute.slsa	3.153	0.361	3.504
wrapper.mvHisto	0.383	0.008	0.392
wrapper.mvHisto_HC	0.404	0.111	0.514
wrapper.mvImage	0.945	0.081	1.025
wrapper.mvPerLinesHisto	0.348	0.012	0.360
wrapper.mvPerLinesHistoPerCondition	0.369	0.011	0.380
wrapper.mvPerLinesHistoPerCondition_HC	0.477	0.105	0.593
wrapper.mvPerLinesHisto_HC	0.263	0.013	0.275
wrapper.normalizeD	0.413	0.021	0.433
wrapper.pca	0.411	0.015	0.425
wrapper.t_test_Complete	0.650	0.042	0.692
wrapperCalibrationPlot	0.346	0.025	0.372
writeMSnsetToCSV	0.001	0.000	0.000
writeMSnsetToExcel	0.000	0.001	0.001

CHECK report for DAPAR on celaya2

Summary

Command output

Installation output

Tests output

Example timings