Multiple platform build/check report for BioC 3.15 - CHECK results for DAPAR on palomino3

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 20.04.5 LTS)	x86_64	4.2.1 (2022-06-23) -- "Funny-Looking Kid"	4386
palomino3	Windows Server 2022 Datacenter	x64	4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid"	4138
merida1	macOS 10.14.6 Mojave	x86_64	4.2.1 (2022-06-23) -- "Funny-Looking Kid"	4205
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

Package: DAPAR

Version: 1.28.5

Command: F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:DAPAR.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings DAPAR_1.28.5.tar.gz

StartedAt: 2022-10-18 23:25:16 -0400 (Tue, 18 Oct 2022)

EndedAt: 2022-10-18 23:35:09 -0400 (Tue, 18 Oct 2022)

EllapsedTime: 593.8 seconds

RetCode: 0

Status: OK

CheckDir: DAPAR.Rcheck

Warnings: 0

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###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:DAPAR.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings DAPAR_1.28.5.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/DAPAR.Rcheck'
* using R version 4.2.1 (2022-06-23 ucrt)
* using platform: x86_64-w64-mingw32 (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 '1.28.5'
* package encoding: UTF-8
* 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 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
GetIndices_MetacellFiltering: no visible global function definition for
  'tsop'
aggregateIterParallel: no visible binding for global variable 'cond'
averageIntensities: no visible binding for global variable 'condition'
averageIntensities: no visible binding for global variable 'feature'
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'
display.CC.visNet: no visible binding for global variable
  'layout_nicely'
getTextForGOAnalysis: no visible binding for global variable
  'textGOParams'
getTextForGOAnalysis: no visible binding for global variable 'input'
heatmapForMissingValues: no visible binding for global variable 'par'
limmaCompleteTest: no visible binding for global variable 'A'
limmaCompleteTest: no visible binding for global variable 'B'
limmaCompleteTest: no visible binding for global variable 'P.Value'
pepa.test: no visible global function definition for 'nodes<-'
visualizeClusters: no visible binding for global variable
  'adjusted_pvalues'
visualizeClusters: no visible binding for global variable 'Condition'
visualizeClusters: no visible binding for global variable 'Intensity'
visualizeClusters: no visible binding for global variable
  'FDR_threshold'
visualizeClusters: no visible binding for global variable 'feature'
wrapperClassic1wayAnova: no visible binding for global variable
  'Pr(>F)1'
wrapperRunClustering: no visible global function definition for 'str_c'
Undefined global functions or variables:
  A B Condition FDR_threshold Intensity P.Value Pr(>F)1
  adjusted_pvalues cond condition feature g input layout_nicely nodes<-
  par str_c textGOParams tsop x y
Consider adding
  importFrom("graphics", "par")
to your NAMESPACE file.
* 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 (user + system) or elapsed time > 5s
                                   user system elapsed
wrapper.compareNormalizationD_HC 188.59   6.03  196.19
wrapper.dapar.impute.mi           28.42   0.48   28.96
metacombine                       10.25   0.28   10.56
barplotEnrichGO_HC                 8.41   0.53    9.00
scatterplotEnrichGO_HC             6.54   0.29    6.88
barplotGroupGO_HC                  5.93   0.44    6.39
group_GO                           4.92   0.22    5.14
enrich_GO                          4.68   0.37    5.06
CVDistD_HC                         2.75   0.35    5.79
BuildMetaCell                      1.39   0.07    5.66
aggregateIterParallel              1.28   0.03    9.95
BuildColumnToProteinDataset_par    1.00   0.13   20.08
* 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
  'F:/biocbuild/bbs-3.15-bioc/meat/DAPAR.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL DAPAR
###
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* installing to library 'F:/biocbuild/bbs-3.15-bioc/R/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)


R version 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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)

This is the 'DAPAR' version 1.28.5.

  To get started, visit
    http://www.prostar-proteomics.org/


> 
> test_check("DAPAR")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
> 
> proc.time()
   user  system elapsed 
   8.40    0.71    9.95

name	user	system	elapsed
AggregateMetacell	2.88	0.11	3.00
BuildAdjacencyMatrix	0.39	0.00	0.39
BuildColumnToProteinDataset	1.10	0.00	1.11
BuildColumnToProteinDataset_par	1.00	0.13	20.08
BuildMetaCell	1.39	0.07	5.66
CVDistD_HC	2.75	0.35	5.79
CountPep	0.41	0.00	0.41
ExtendPalette	0.01	0.01	0.03
GOAnalysisSave	0	0	0
GetCC	1.84	0.03	1.88
GetColorsForConditions	0.45	0.00	0.46
GetDetailedNbPeptides	0.43	0.02	0.43
GetDetailedNbPeptidesUsed	0	0	0
GetIndices_BasedOnConditions	0.53	0.03	0.57
GetIndices_MetacellFiltering	0.50	0.03	0.53
GetIndices_WholeLine	0.50	0.02	0.51
GetIndices_WholeMatrix	0.54	0.01	0.56
GetKeyId	0.47	0.03	0.50
GetMatAdj	0.52	0.00	0.52
GetMetacell	0	0	0
GetNbPeptidesUsed	0.51	0.07	0.58
GetTypeofData	0.38	0.04	0.42
Get_AllComparisons	0.30	0.02	0.33
GlobalQuantileAlignment	0.53	0.02	0.55
GraphPepProt	0.40	0.03	0.43
LH0	0	0	0
LH0.lm	0	0	0
LH1	0	0	0
LH1.lm	0	0	0
LOESS	1.25	0.00	1.25
MeanCentering	0.45	0.01	0.47
MetaCellFiltering	0.50	0.03	0.53
MetacellFilteringScope	0	0	0
Metacell_generic	0.69	0.05	0.73
Metacell_maxquant	0.64	0.00	0.64
Metacell_proline	0.64	0.00	0.65
NumericalFiltering	0.52	0.00	0.51
NumericalgetIndicesOfLinesToRemove	0.40	0.00	0.41
QuantileCentering	0.44	0.00	0.43
SetCC	1.58	0.02	1.60
SetMatAdj	0.39	0.01	0.40
Set_POV_MEC_tags	0.47	0.01	0.48
StringBasedFiltering	0.61	0.02	0.63
StringBasedFiltering2	0.61	0.00	0.61
SumByColumns	1.61	0.03	1.65
SymFilteringOperators	0	0	0
UpdateMetacell	0	0	0
aggregateIter	1.24	0.01	1.25
aggregateIterParallel	1.28	0.03	9.95
aggregateMean	1.07	0.00	1.08
aggregateSum	1.74	0.03	1.77
aggregateTopn	1.20	0.04	1.23
averageIntensities	0.47	0.17	0.64
barplotEnrichGO_HC	8.41	0.53	9.00
barplotGroupGO_HC	5.93	0.44	6.39
boxPlotD_HC	0.22	0.11	0.33
buildGraph	1.45	0.00	1.45
check.conditions	0.49	0.00	0.48
check.design	0.39	0.00	0.41
checkClusterability	0.23	0.03	0.27
classic1wayAnova	1.24	0.03	1.26
compareNormalizationD_HC	0.20	0.08	0.33
compute_t_tests	1.03	0.00	1.03
corrMatrixD_HC	0.42	0.12	0.56
createMSnset	2.13	0.02	2.14
dapar_hc_ExportMenu	0.14	0.25	0.47
dapar_hc_chart	0.08	0.03	0.13
deleteLinesFromIndices	0.4	0.0	0.4
densityPlotD_HC	2.19	0.25	2.47
diffAnaComputeFDR	0.44	0.06	0.52
diffAnaGetSignificant	0.29	0.02	0.31
diffAnaSave	0.27	0.00	0.27
diffAnaVolcanoplot	0.22	0.01	0.23
diffAnaVolcanoplot_rCharts	0.33	0.08	0.44
display.CC.visNet	1.54	0.05	1.91
enrich_GO	4.68	0.37	5.06
finalizeAggregation	0	0	0
findMECBlock	1.34	0.00	1.35
formatLimmaResult	0.16	0.00	0.15
formatPHResults	3.01	0.10	3.12
fudge2LRT	0	0	0
get.pep.prot.cc	1.27	0.00	1.27
getIndicesConditions	0.33	0.00	0.33
getIndicesOfLinesToRemove	0.37	0.00	0.37
getListNbValuesInLines	0.45	0.00	0.46
getNumberOf	0.54	0.00	0.53
getNumberOfEmptyLines	0.5	0.0	0.5
getPourcentageOfMV	0.42	0.00	0.42
getProcessingInfo	0.43	0.00	0.44
getProteinsStats	0.52	0.01	0.53
getQuantile4Imp	0.14	0.00	0.14
getTextForAggregation	0	0	0
getTextForAnaDiff	0	0	0
getTextForFiltering	0	0	0
getTextForGOAnalysis	0	0	0
getTextForHypothesisTest	0	0	0
getTextForNewDataset	0	0	0
getTextForNormalization	0	0	0
getTextForpeptideImputation	0	0	0
getTextForproteinImputation	0	0	0
group_GO	4.92	0.22	5.14
hc_logFC_DensityPlot	1.33	0.12	1.48
hc_mvTypePlot2	0.84	0.09	0.99
heatmapD	0.80	0.07	0.86
heatmapForMissingValues	0.22	0.00	0.22
histPValue_HC	0.31	0.13	0.44
impute.pa2	0.55	0.01	0.56
inner.aggregate.iter	0.43	0.02	0.46
inner.aggregate.topn	0.46	0.00	0.45
inner.mean	0.34	0.00	0.34
inner.sum	0.39	0.00	0.39
limmaCompleteTest	1.23	0.05	1.28
listSheets	0	0	0
make.contrast	0.33	0.00	0.33
make.design.1	0.50	0.04	0.55
make.design.2	0.44	0.02	0.45
make.design.3	0.39	0.01	0.40
make.design	0.43	0.00	0.44
match.metacell	0.49	0.02	0.50
metacell.def	0	0	0
metacellHisto_HC	0.36	0.09	0.47
metacellPerLinesHistoPerCondition_HC	0.64	0.16	0.83
metacellPerLinesHisto_HC	0.64	0.06	0.70
metacombine	10.25	0.28	10.56
mvImage	2.27	0.07	2.33
my_hc_ExportMenu	0.14	0.31	0.46
my_hc_chart	0.15	0.22	0.41
nonzero	0.01	0.00	0.01
normalizeMethods.dapar	0	0	0
pepa.test	0.50	0.03	0.53
plotJitter	1.38	0.00	1.38
plotJitter_rCharts	1.51	0.09	1.61
plotPCA_Eigen	0.57	0.02	0.58
plotPCA_Eigen_hc	0.42	0.01	0.43
plotPCA_Ind	0.44	0.02	0.46
plotPCA_Var	0.48	0.02	0.50
postHocTest	3.20	0.11	3.32
proportionConRev_HC	0.07	0.06	0.13
rbindMSnset	0.54	0.00	0.55
reIntroduceMEC	0.55	0.00	0.54
readExcel	0	0	0
removeLines	0.55	0.00	0.55
samLRT	0	0	0
saveParameters	0.39	0.00	0.39
scatterplotEnrichGO_HC	6.54	0.29	6.88
search.metacell.tags	0	0	0
splitAdjacencyMat	0.52	0.02	0.53
test.design	0.43	0.00	0.44
translatedRandomBeta	0	0	0
univ_AnnotDbPkg	0.16	0.05	0.20
violinPlotD	0.32	0.00	0.36
visualizeClusters	1.25	0.03	1.29
vsn	0.88	0.00	0.88
wrapper.CVDistD_HC	1.28	0.06	1.39
wrapper.compareNormalizationD_HC	188.59	6.03	196.19
wrapper.corrMatrixD_HC	0.55	0.10	0.65
wrapper.dapar.impute.mi	28.42	0.48	28.96
wrapper.heatmapD	0.66	0.02	0.67
wrapper.impute.KNN	0.47	0.00	0.47
wrapper.impute.detQuant	0.59	0.03	0.62
wrapper.impute.fixedValue	0.58	0.00	0.58
wrapper.impute.mle	0.53	0.00	0.53
wrapper.impute.pa	0.19	0.01	0.21
wrapper.impute.pa2	0.58	0.05	0.62
wrapper.impute.slsa	0.64	0.00	0.64
wrapper.mvImage	0.22	0.00	0.22
wrapper.normalizeD	0.51	0.02	0.53
wrapper.pca	0.22	0.00	0.22
wrapperCalibrationPlot	0.25	0.01	0.27
wrapperClassic1wayAnova	1.59	0.05	1.64
wrapperRunClustering	2.14	0.05	2.18
write.excel	0.78	0.03	0.88
writeMSnsetToCSV	0.50	0.02	0.65
writeMSnsetToExcel	0.92	0.08	1.11

CHECK results for DAPAR on palomino3

Summary

Command output

Installation output

Tests output

Example timings