Multiple platform build/check report for BioC 3.8 - CHECK report for DAPAR on malbec1

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:DAPAR.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings DAPAR_1.14.5.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/DAPAR.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.14.5’
* 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 ... 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’
Undefined global functions or variables:
  cond conds g input textGOParams 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                                   user system elapsed
wrapper.compareNormalizationD_HC 45.288  2.060  48.135
wrapper.dapar.impute.mi          12.168  0.200  12.543
CVDistD                           6.756  0.404   7.264
wrapper.CVDistD                   6.712  0.252   7.020
aggregateIter                     5.068  0.180   5.286
* 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
  ‘/home/biocbuild/bbs-3.8-bioc/meat/DAPAR.Rcheck/00check.log’
for details.

Installation output

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL DAPAR
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/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 version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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

> 
> test_check("DAPAR")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 3 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 13.084   0.368  13.523

Example timings

name	user	system	elapsed
BuildAdjacencyMatrix	1.304	0.112	1.440
BuildColumnToProteinDataset	2.568	0.132	2.756
BuildColumnToProteinDataset_par	1.516	0.596	1.365
CVDistD	6.756	0.404	7.264
CVDistD_HC	3.840	0.160	4.366
CountPep	0.584	0.088	0.674
GraphPepProt	0.472	0.028	0.500
StringBasedFiltering	0.640	0.016	0.665
StringBasedFiltering2	0.560	0.008	0.572
addOriginOfValue	0.372	0.000	0.374
aggregateIter	5.068	0.180	5.286
aggregateIterParallel	3.828	1.108	3.116
aggregateMean	0.536	0.040	0.582
aggregateSum	0.600	0.016	0.625
aggregateTopn	2.704	0.152	2.886
boxPlotD	0.444	0.008	0.452
boxPlotD_HC	1.844	0.100	2.007
check.conditions	0.384	0.004	0.390
check.design	0.392	0.000	0.394
compareNormalizationD	0.628	0.016	0.645
compareNormalizationD_HC	3.472	0.132	3.677
compute.t.tests	0.776	0.016	0.793
corrMatrixD	0.896	0.012	0.912
corrMatrixD_HC	0.452	0.028	0.481
createMSnset	0.940	0.036	1.010
deleteLinesFromIndices	0.432	0.012	0.446
densityPlotD	0.452	0.004	0.455
densityPlotD_HC	2.172	0.104	2.276
diffAnaComputeFDR	0.412	0.008	0.421
diffAnaGetSignificant	0.752	0.000	0.761
diffAnaSave	0.684	0.008	0.690
diffAnaVolcanoplot	0.456	0.004	0.458
diffAnaVolcanoplot_rCharts	0	0	0
enrich_GO	0	0	0
findMECBlock	0.388	0.004	0.393
formatLimmaResult	0.536	0.004	0.541
getIndicesConditions	0.380	0.000	0.382
getIndicesOfLinesToRemove	0.216	0.000	0.219
getListNbValuesInLines	0.300	0.004	0.307
getNumberOf	0.372	0.004	0.377
getNumberOfEmptyLines	0.444	0.004	0.447
getPourcentageOfMV	0.380	0.004	0.384
getProcessingInfo	0.380	0.004	0.384
getProteinsStats	0.480	0.016	0.496
getQuantile4Imp	0.384	0.004	0.390
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	0.004	0.000	0.002
getTextForNormalization	0.000	0.000	0.001
getTextForpeptideImputation	0.000	0.000	0.001
getTextForproteinImputation	0	0	0
group_GO	0	0	0
hc_logFC_DensityPlot	0.852	0.048	0.903
hc_mvTypePlot2	2.960	0.096	3.075
heatmap.DAPAR	0.748	0.004	0.751
heatmapD	1.228	0.032	1.265
impute.detQuant	0.724	0.188	0.925
impute.pa2	0.604	0.012	0.617
is.MV	0.640	0.232	0.875
is.OfType	0.636	0.216	0.863
limmaCompleteTest	0.572	0.012	0.590
make.contrast	0.380	0.000	0.381
make.design.1	0.392	0.004	0.397
make.design.2	0.000	0.000	0.001
make.design.3	0	0	0
make.design	0.368	0.008	0.380
mvFilter	0.496	0.004	0.501
mvFilterFromIndices	0.392	0.004	0.393
mvFilterGetIndices	0.528	0.080	0.611
mvHisto	0.440	0.004	0.447
mvHisto_HC	0.444	0.020	0.467
mvImage	3.920	0.144	4.148
mvPerLinesHisto	0.504	0.008	0.512
mvPerLinesHistoPerCondition	0.444	0.004	0.450
mvPerLinesHistoPerCondition_HC	0.536	0.020	0.555
mvPerLinesHisto_HC	0.468	0.004	0.476
my_hc_ExportMenu	0.148	0.036	0.207
my_hc_chart	0.156	0.028	0.190
nonzero	0.028	0.000	0.030
plotPCA_Eigen	0.372	0.000	0.379
plotPCA_Eigen_hc	0.380	0.000	0.382
plotPCA_Ind	0.412	0.004	0.416
plotPCA_Var	0.380	0.000	0.381
proportionConRev_HC	0.052	0.012	0.062
rbindMSnset	0.396	0.020	0.416
reIntroduceMEC	0.608	0.000	0.611
removeLines	0.376	0.012	0.386
saveParameters	0.384	0.004	0.390
setMEC	0.600	0.004	0.604
test.design	0.384	0.000	0.382
translatedRandomBeta	0.000	0.004	0.006
violinPlotD	1.012	0.008	1.020
wrapper.CVDistD	6.712	0.252	7.020
wrapper.CVDistD_HC	3.784	0.168	3.950
wrapper.compareNormalizationD	0.620	0.008	0.631
wrapper.compareNormalizationD_HC	45.288	2.060	48.135
wrapper.corrMatrixD	0.788	0.004	0.793
wrapper.corrMatrixD_HC	0.480	0.016	0.500
wrapper.dapar.impute.mi	12.168	0.200	12.543
wrapper.hc_mvTypePlot2	3.076	0.140	3.251
wrapper.heatmapD	1.100	0.040	1.167
wrapper.impute.KNN	0.428	0.004	0.434
wrapper.impute.detQuant	0.440	0.004	0.444
wrapper.impute.fixedValue	0.424	0.008	0.433
wrapper.impute.mle	0.420	0.008	0.429
wrapper.impute.pa	1.248	0.004	1.261
wrapper.impute.pa2	0.612	0.008	0.621
wrapper.impute.slsa	2.048	0.040	2.109
wrapper.mvHisto	0.412	0.012	0.426
wrapper.mvHisto_HC	0.428	0.012	0.440
wrapper.mvImage	2.976	0.100	3.102
wrapper.mvPerLinesHisto	0.288	0.004	0.294
wrapper.mvPerLinesHistoPerCondition	0.364	0.000	0.365
wrapper.mvPerLinesHistoPerCondition_HC	0.428	0.012	0.441
wrapper.mvPerLinesHisto_HC	0.236	0.000	0.238
wrapper.normalizeD	0.240	0.012	0.252
wrapper.pca	0.252	0.000	0.255
wrapper.t_test_Complete	0.620	0.012	0.640
wrapperCalibrationPlot	0.468	0.004	0.480
writeMSnsetToCSV	0.000	0.000	0.001
writeMSnsetToExcel	0.000	0.000	0.001

CHECK report for DAPAR on malbec1

Summary

Command output

Installation output

Tests output

Example timings