Multiple platform build/check report for BioC 3.8 - CHECK report for DAPAR on merida1

##############################################################################
##############################################################################
###
### Running 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_1.14.5.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/DAPAR.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.14.5’
* 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 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 62.957  5.043  67.613
wrapper.dapar.impute.mi          13.998  0.926  14.915
CVDistD                           9.545  1.020  10.502
wrapper.CVDistD                   9.069  0.763   9.762
aggregateIterParallel             4.725  2.448   4.165
CVDistD_HC                        5.498  0.514   5.984
wrapper.CVDistD_HC                5.396  0.478   5.839
mvImage                           4.951  0.297   5.233
wrapper.mvImage                   4.888  0.287   5.165
* 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-3.8-bioc/meat/DAPAR.Rcheck/00check.log’
for details.

Installation output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL DAPAR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/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 version 3.5.3 (2019-03-11) -- "Great Truth"
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 
 12.597   0.852  13.522

Example timings

name	user	system	elapsed
BuildAdjacencyMatrix	1.212	0.214	1.427
BuildColumnToProteinDataset	2.364	0.302	2.671
BuildColumnToProteinDataset_par	1.724	0.746	1.206
CVDistD	9.545	1.020	10.502
CVDistD_HC	5.498	0.514	5.984
CountPep	0.585	0.175	0.762
GraphPepProt	0.483	0.054	0.543
StringBasedFiltering	0.746	0.062	0.814
StringBasedFiltering2	0.458	0.038	0.499
addOriginOfValue	0.833	0.018	0.864
aggregateIter	4.192	0.419	4.674
aggregateIterParallel	4.725	2.448	4.165
aggregateMean	0.532	0.041	0.577
aggregateSum	0.580	0.035	0.617
aggregateTopn	2.586	0.185	2.767
boxPlotD	0.430	0.014	0.448
boxPlotD_HC	2.203	0.263	2.462
check.conditions	0.311	0.004	0.322
check.design	0.348	0.006	0.361
compareNormalizationD	0.471	0.028	0.503
compareNormalizationD_HC	4.591	0.404	4.969
compute.t.tests	0.847	0.049	0.896
corrMatrixD	0.821	0.044	0.872
corrMatrixD_HC	0.463	0.058	0.524
createMSnset	0.998	0.083	1.083
deleteLinesFromIndices	0.522	0.014	0.537
densityPlotD	0.331	0.009	0.344
densityPlotD_HC	2.537	0.241	2.774
diffAnaComputeFDR	0.512	0.013	0.528
diffAnaGetSignificant	0.778	0.033	0.812
diffAnaSave	0.697	0.040	0.741
diffAnaVolcanoplot	0.401	0.012	0.414
diffAnaVolcanoplot_rCharts	0	0	0
enrich_GO	0.000	0.000	0.001
findMECBlock	0.389	0.009	0.398
formatLimmaResult	0.507	0.017	0.528
getIndicesConditions	0.331	0.005	0.342
getIndicesOfLinesToRemove	0.342	0.005	0.348
getListNbValuesInLines	0.969	0.096	1.071
getNumberOf	0.323	0.004	0.327
getNumberOfEmptyLines	0.381	0.010	0.399
getPourcentageOfMV	0.349	0.011	0.362
getProcessingInfo	0.299	0.006	0.307
getProteinsStats	0.368	0.022	0.394
getQuantile4Imp	0.386	0.012	0.402
getTextForAggregation	0	0	0
getTextForAnaDiff	0.001	0.000	0.001
getTextForFiltering	0.001	0.000	0.000
getTextForGOAnalysis	0	0	0
getTextForHypothesisTest	0.001	0.000	0.000
getTextForNewDataset	0.002	0.002	0.005
getTextForNormalization	0.001	0.000	0.001
getTextForpeptideImputation	0.001	0.001	0.001
getTextForproteinImputation	0.000	0.000	0.001
group_GO	0.000	0.000	0.001
hc_logFC_DensityPlot	0.704	0.080	0.789
hc_mvTypePlot2	3.884	0.310	4.175
heatmap.DAPAR	0.547	0.026	0.574
heatmapD	1.286	0.074	1.368
impute.detQuant	0.922	0.526	1.443
impute.pa2	0.603	0.032	0.635
is.MV	0.884	0.550	1.436
is.OfType	0.909	0.555	1.460
limmaCompleteTest	0.471	0.017	0.489
make.contrast	0.354	0.007	0.363
make.design.1	0.306	0.005	0.317
make.design.2	0	0	0
make.design.3	0.001	0.000	0.000
make.design	0.328	0.006	0.338
mvFilter	0.409	0.015	0.425
mvFilterFromIndices	0.378	0.007	0.390
mvFilterGetIndices	0.514	0.125	0.640
mvHisto	0.355	0.008	0.369
mvHisto_HC	0.421	0.047	0.474
mvImage	4.951	0.297	5.233
mvPerLinesHisto	0.381	0.018	0.404
mvPerLinesHistoPerCondition	0.343	0.008	0.355
mvPerLinesHistoPerCondition_HC	0.488	0.051	0.544
mvPerLinesHisto_HC	0.430	0.051	0.484
my_hc_ExportMenu	0.167	0.118	0.290
my_hc_chart	0.174	0.139	0.321
nonzero	0.025	0.001	0.026
plotPCA_Eigen	0.347	0.004	0.357
plotPCA_Eigen_hc	0.347	0.005	0.356
plotPCA_Ind	0.334	0.005	0.344
plotPCA_Var	0.288	0.005	0.294
proportionConRev_HC	0.054	0.042	0.098
rbindMSnset	0.396	0.017	0.412
reIntroduceMEC	0.620	0.026	0.646
removeLines	0.319	0.005	0.326
saveParameters	0.315	0.004	0.323
setMEC	0.498	0.017	0.520
test.design	0.304	0.005	0.311
translatedRandomBeta	0.006	0.006	0.012
violinPlotD	1.033	0.026	1.065
wrapper.CVDistD	9.069	0.763	9.762
wrapper.CVDistD_HC	5.396	0.478	5.839
wrapper.compareNormalizationD	0.494	0.018	0.516
wrapper.compareNormalizationD_HC	62.957	5.043	67.613
wrapper.corrMatrixD	0.843	0.043	0.888
wrapper.corrMatrixD_HC	0.403	0.051	0.467
wrapper.dapar.impute.mi	13.998	0.926	14.915
wrapper.hc_mvTypePlot2	4.475	0.300	4.762
wrapper.heatmapD	1.637	0.074	1.722
wrapper.impute.KNN	0.340	0.008	0.349
wrapper.impute.detQuant	0.362	0.007	0.377
wrapper.impute.fixedValue	0.348	0.008	0.361
wrapper.impute.mle	0.362	0.011	0.380
wrapper.impute.pa	0.652	0.041	0.694
wrapper.impute.pa2	0.396	0.024	0.418
wrapper.impute.slsa	2.217	0.112	2.321
wrapper.mvHisto	0.345	0.009	0.358
wrapper.mvHisto_HC	0.397	0.063	0.463
wrapper.mvImage	4.888	0.287	5.165
wrapper.mvPerLinesHisto	0.367	0.018	0.389
wrapper.mvPerLinesHistoPerCondition	0.344	0.007	0.359
wrapper.mvPerLinesHistoPerCondition_HC	0.440	0.052	0.496
wrapper.mvPerLinesHisto_HC	0.329	0.011	0.341
wrapper.normalizeD	0.319	0.009	0.329
wrapper.pca	0.324	0.005	0.332
wrapper.t_test_Complete	0.573	0.025	0.600
wrapperCalibrationPlot	0.461	0.013	0.477
writeMSnsetToCSV	0	0	0
writeMSnsetToExcel	0	0	0

CHECK report for DAPAR on merida1

Summary

Command output

Installation output

Tests output

Example timings