Multiple platform build/check report for BioC 3.7 - 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_1.12.11.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/DAPAR.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.12.11’
* 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
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:
  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 61.453  5.077  66.117
wrapper.dapar.impute.mi          13.504  0.987  14.472
wrapper.CVDistD                   8.863  0.764   9.560
CVDistD                           6.879  0.148   7.101
wrapper.CVDistD_HC                5.440  0.472   5.891
wrapper.mvImage                   4.916  0.292   5.191
* 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-3.7-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/3.5/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 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
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)

> 
> test_check("DAPAR")
1 2 3 4 5   
5 2 2 4 1 0 
1 2 3 4 5   
5 2 2 4 1 0 
1 2 3 4 5   
5 2 2 4 1 0 
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 41 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 14.283   0.659  15.874

Example timings

name	user	system	elapsed
BuildAdjacencyMatrix	1.182	0.114	1.301
BuildColumnToProteinDataset	1.037	0.034	1.077
BuildColumnToProteinDataset_par	1.584	0.541	1.068
CVDistD	6.879	0.148	7.101
CVDistD_HC	4.456	0.136	4.646
CountPep	0.484	0.103	0.590
GraphPepProt	0.372	0.020	0.396
MeanPeptides	0.365	0.042	0.411
StringBasedFiltering	0.526	0.040	0.567
StringBasedFiltering2	0.361	0.017	0.378
SumPeptides	0.417	0.054	0.478
TopnPeptides	2.306	0.064	2.402
addOriginOfValue	0.359	0.004	0.370
boxPlotD	0.319	0.008	0.326
boxPlotD_HC	1.584	0.039	1.640
buildLogText	0.003	0.001	0.004
check.conditions	0.297	0.005	0.303
check.design	0.315	0.004	0.322
compareNormalizationD	0.416	0.021	0.441
compareNormalizationD_HC	3.312	0.049	3.406
compute.t.tests	0.752	0.012	0.771
corrMatrixD	0.757	0.023	0.796
corrMatrixD_HC	0.450	0.026	0.479
createMSnset	0.883	0.019	0.912
deleteLinesFromIndices	0.437	0.007	0.448
densityPlotD	0.388	0.011	0.402
densityPlotD_HC	2.168	0.043	2.237
diffAnaComputeFDR	0.448	0.006	0.457
diffAnaGetSignificant	0.701	0.016	0.730
diffAnaSave	1.179	0.024	1.217
diffAnaVolcanoplot	0.411	0.004	0.420
diffAnaVolcanoplot_rCharts	0.000	0.000	0.001
enrich_GO	0.001	0.000	0.000
findMECBlock	0.309	0.004	0.317
formatLimmaResult	0.451	0.008	0.462
getIndicesConditions	0.308	0.003	0.315
getIndicesOfLinesToRemove	0.366	0.004	0.377
getListNbValuesInLines	0.337	0.004	0.346
getNumberOf	0.367	0.006	0.376
getNumberOfEmptyLines	0.331	0.004	0.335
getPaletteForLabels	0.306	0.003	0.313
getPaletteForLabels_HC	0.328	0.003	0.334
getPaletteForReplicates	0.306	0.003	0.315
getPaletteForReplicates_HC	0.355	0.004	0.362
getPourcentageOfMV	0.383	0.009	0.397
getProcessingInfo	0.306	0.004	0.311
getProteinsStats	0.361	0.012	0.376
getQuantile4Imp	0.338	0.005	0.345
getTextForAggregation	0.002	0.000	0.002
getTextForAnaDiff	0.004	0.002	0.006
getTextForFiltering	0.002	0.000	0.003
getTextForGOAnalysis	0.001	0.000	0.002
getTextForImputation	0.004	0.002	0.007
getTextForNewDataset	0.002	0.001	0.003
getTextForNormalization	0.002	0.000	0.002
group_GO	0.001	0.000	0.001
hc_FC_DensityPlot	0.699	0.023	0.727
hc_mvTypePlot2	3.552	0.048	3.635
heatmap.DAPAR	0.618	0.018	0.644
heatmapD	1.104	0.040	1.158
impute.detQuant	0.796	0.381	1.185
impute.pa2	0.510	0.014	0.526
is.MV	0.808	0.424	1.251
is.OfType	0.769	0.413	1.195
limmaCompleteTest	0.441	0.008	0.452
make.contrast	0.324	0.004	0.330
make.design.1	0.304	0.004	0.309
make.design.2	0.001	0.000	0.001
make.design.3	0.001	0.000	0.001
make.design	0.313	0.005	0.320
mvFilter	0.365	0.004	0.374
mvFilterFromIndices	0.345	0.005	0.351
mvFilterGetIndices	0.469	0.085	0.560
mvHisto	0.409	0.010	0.425
mvHisto_HC	0.372	0.018	0.399
mvImage	3.798	0.023	3.860
mvImputation	0.337	0.010	0.351
mvPerLinesHisto	0.434	0.014	0.454
mvPerLinesHistoPerCondition	0.337	0.011	0.353
mvPerLinesHistoPerCondition_HC	0.408	0.024	0.435
mvPerLinesHisto_HC	0.380	0.040	0.422
mvTypePlot	1.613	0.028	1.646
my_hc_ExportMenu	0.138	0.057	0.199
my_hc_chart	0.145	0.074	0.264
nonzero	0.021	0.001	0.022
normalizeD	0.418	0.033	0.460
pepAgregate	0.484	0.016	0.505
proportionConRev_HC	0.055	0.022	0.078
rbindMSnset	0.336	0.005	0.346
reIntroduceMEC	0.524	0.007	0.535
removeLines	0.340	0.004	0.352
saveParameters	0.299	0.004	0.308
setMEC	0.442	0.005	0.448
test.design	0.327	0.004	0.336
translatedRandomBeta	0.005	0.004	0.009
violinPlotD	1.522	0.040	1.586
wrapper.CVDistD	8.863	0.764	9.560
wrapper.CVDistD_HC	5.440	0.472	5.891
wrapper.boxPlotD	0.361	0.011	0.375
wrapper.boxPlotD_HC	2.581	0.199	2.788
wrapper.compareNormalizationD	0.476	0.019	0.505
wrapper.compareNormalizationD_HC	61.453	5.077	66.117
wrapper.corrMatrixD	0.931	0.049	0.981
wrapper.corrMatrixD_HC	0.489	0.038	0.535
wrapper.dapar.impute.mi	13.504	0.987	14.472
wrapper.densityPlotD	0.376	0.009	0.394
wrapper.densityPlotD_HC	2.710	0.225	2.927
wrapper.hc_mvTypePlot2	4.015	0.303	4.305
wrapper.heatmapD	1.145	0.066	1.216
wrapper.impute.KNN	0.425	0.008	0.435
wrapper.impute.detQuant	0.360	0.007	0.370
wrapper.impute.fixedValue	0.350	0.008	0.359
wrapper.impute.pa	0.614	0.036	0.650
wrapper.impute.pa2	0.602	0.031	0.635
wrapper.impute.slsa	2.771	0.131	2.898
wrapper.mvHisto	0.318	0.009	0.332
wrapper.mvHisto_HC	0.336	0.006	0.343
wrapper.mvImage	4.916	0.292	5.191
wrapper.mvImputation	0.379	0.007	0.387
wrapper.mvPerLinesHisto	0.415	0.016	0.435
wrapper.mvPerLinesHistoPerCondition	0.365	0.006	0.374
wrapper.mvPerLinesHistoPerCondition_HC	0.391	0.009	0.403
wrapper.mvPerLinesHisto_HC	0.329	0.011	0.343
wrapper.mvTypePlot	2.036	0.092	2.128
wrapper.normalizeD	0.372	0.007	0.379
wrapper.t_test_Complete	0.584	0.023	0.612
wrapper.violinPlotD	1.338	0.023	1.380
wrapperCalibrationPlot	0.385	0.010	0.397
writeMSnsetToCSV	0.001	0.000	0.001
writeMSnsetToExcel	0.000	0.000	0.001

CHECK report for DAPAR on merida2

Summary

Command output

Installation output

Tests output

Example timings