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This page was generated on 2025-09-24 12:05 -0400 (Wed, 24 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4827
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4614
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4558
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4560
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 516/2334HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DAPAR 1.41.0  (landing page)
Samuel Wieczorek
Snapshot Date: 2025-09-23 13:45 -0400 (Tue, 23 Sep 2025)
git_url: https://git.bioconductor.org/packages/DAPAR
git_branch: devel
git_last_commit: c47beab
git_last_commit_date: 2025-04-15 10:53:48 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for DAPAR on lconway

To the developers/maintainers of the DAPAR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DAPAR.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: DAPAR
Version: 1.41.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DAPAR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DAPAR_1.41.0.tar.gz
StartedAt: 2025-09-23 20:29:15 -0400 (Tue, 23 Sep 2025)
EndedAt: 2025-09-23 20:40:08 -0400 (Tue, 23 Sep 2025)
EllapsedTime: 653.2 seconds
RetCode: 0
Status:   OK  
CheckDir: DAPAR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DAPAR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DAPAR_1.41.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/DAPAR.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DAPAR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DAPAR’ version ‘1.41.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Vignette dependency required without any vignettes: ‘knitr’
* 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 DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code 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 whether startup messages can be suppressed ... 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
Check_Dataset_Validity: no visible global function definition for
  ‘exprs’
OWAnova: no visible global function definition for ‘aov’
aggregateIterParallel: no visible binding for global variable ‘cond’
averageIntensities: no visible binding for global variable ‘condition’
averageIntensities: no visible binding for global variable ‘feature’
averageIntensities: no visible binding for global variable ‘intensity’
createMSnset: no visible global function definition for
  ‘installed.packages’
createMSnset: no visible binding for global variable ‘Prostar.loc’
createMSnset2: no visible global function definition for
  ‘installed.packages’
createMSnset2: no visible binding for global variable ‘Prostar.loc’
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’
globalAdjPval: no visible global function definition for ‘stack’
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<-’
testAnovaModels : <anonymous>: no visible global function definition
  for ‘TukeyHSD’
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 Prostar.loc
  TukeyHSD adjusted_pvalues aov cond condition exprs feature g input
  installed.packages intensity layout_nicely nodes<- par stack str_c
  textGOParams x y
Consider adding
  importFrom("graphics", "par")
  importFrom("stats", "TukeyHSD", "aov")
  importFrom("utils", "installed.packages", "stack")
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 examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                   user system elapsed
wrapper.compareNormalizationD_HC 62.762 30.593  92.969
wrapper.dapar.impute.mi          15.247  1.275  16.960
barplotEnrichGO_HC                9.775  2.004  11.906
checkClusterability               3.723  2.630   6.543
group_GO                          5.306  0.770   6.174
barplotGroupGO_HC                 5.215  0.762   6.035
scatterplotEnrichGO_HC            5.139  0.673   5.874
enrich_GO                         5.030  0.618   5.695
densityPlotD_HC                   3.617  1.649   5.276
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/DAPAR.Rcheck/00check.log’
for details.


Installation output

DAPAR.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘DAPAR’ ...
** this is package ‘DAPAR’ version ‘1.41.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** 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

DAPAR.Rcheck/tests/testthat.Rout


R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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 1.41.0.

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


> 
> test_check("DAPAR")

 Iterations: 

 1 / 1  - Imputation MNAR OK - 
Imputation MCAR in progress - 
3 % - 6 % - 9 % - 12 % - 15 % - 18 % - 21 % - 24 % - 27 % - 30 % - 33 % - 36 % - 39 % - 42 % - 45 % - 48 % - 51 % - 54 % - 57 % - 60 % - 63 % - 66 % - 69 % - 72 % - 75 % - 78 % - 81 % - 84 % - 87 % - 90 % - 93 % - 96 % - 99 % - 
 Iterations: 

 1 / 1  - Imputation MNAR OK - 
Imputation MCAR in progress - 
3 % - 6 % - 9 % - 12 % - 15 % - 18 % - 21 % - 24 % - 27 % - 30 % - 33 % - 36 % - 39 % - 42 % - 45 % - 48 % - 51 % - 54 % - 57 % - 60 % - 63 % - 66 % - 69 % - 72 % - 75 % - 78 % - 81 % - 84 % - 87 % - 90 % - 93 % - 96 % - 99 % - 
 Imputation in condition  1 ...
 In progress: 10 % - 20 % - 30 % - 40 % - 50 % - 60 % - 70 % - 80 % - 90 % - 100 % - 
 Imputation in condition  2 ...
 In progress: 10 % - 20 % - 30 % - 40 % - 50 % - 60 % - 70 % - 80 % - 90 % - 100 % - [ FAIL 0 | WARN 17 | SKIP 0 | PASS 66 ]

[ FAIL 0 | WARN 17 | SKIP 0 | PASS 66 ]
> 
> proc.time()
   user  system elapsed 
 38.019   1.776  40.283 

Example timings

DAPAR.Rcheck/DAPAR-Ex.timings

nameusersystemelapsed
AggregateMetacell0.6450.0190.666
BuildAdjacencyMatrix0.4980.0070.506
BuildColumnToProteinDataset0.5710.0080.583
BuildMetaCell0.7620.0310.796
CVDistD_HC3.1850.1393.348
Children0.0040.0000.004
CountPep0.4830.0050.490
ExtendPalette0.0270.0010.028
GOAnalysisSave0.0000.0000.001
GetCC2.5570.0222.593
GetColorsForConditions0.4590.0050.467
GetDetailedNbPeptides0.4650.0040.472
GetDetailedNbPeptidesUsed000
GetIndices_BasedOnConditions0.4430.0040.451
GetIndices_MetacellFiltering0.4870.0060.494
GetIndices_WholeLine0.4880.0060.501
GetIndices_WholeMatrix0.4700.0060.480
GetKeyId0.4570.0050.463
GetMatAdj0.5200.0060.527
GetMetacell0.0010.0000.000
GetMetacellTags0.4560.0050.462
GetNbPeptidesUsed0.4620.0060.469
GetNbTags000
GetSoftAvailables0.0010.0000.001
GetTypeofData0.4050.0050.411
Get_AllComparisons0.2680.0160.285
GlobalQuantileAlignment0.4240.0040.430
GraphPepProt0.4630.0040.470
LH0000
LH0.lm000
LH1000
LH1.lm0.0000.0010.000
LOESS1.1200.0161.140
MeanCentering1.3550.0271.391
MetaCellFiltering0.6340.0080.645
MetacellFilteringScope000
Metacell_DIA_NN0.5260.0120.542
Metacell_generic0.5010.0130.517
Metacell_maxquant0.5940.0230.622
Metacell_proline0.5060.0140.523
NumericalFiltering0.5200.0070.530
NumericalgetIndicesOfLinesToRemove0.4720.0060.481
OWAnova0.0050.0010.005
QuantileCentering0.4750.0070.485
SetCC2.3320.0292.376
SetMatAdj0.5230.0060.532
Set_POV_MEC_tags0.4700.0050.479
StringBasedFiltering0.5080.0050.518
StringBasedFiltering20.4880.0040.494
SumByColumns1.5300.0801.626
SymFilteringOperators000
UpdateMetacellAfterImputation0.5050.0090.523
aggregateIter0.6840.0090.701
aggregateIterParallel0.0000.0000.001
aggregateMean0.6030.0070.617
aggregateSum0.5920.0060.603
aggregateTopn0.5430.0060.551
applyAnovasOnProteins0.1350.0040.141
averageIntensities0.6660.1530.829
barplotEnrichGO_HC 9.775 2.00411.906
barplotGroupGO_HC5.2150.7626.035
boxPlotD_HC0.3020.1000.403
buildGraph1.7090.0421.761
check.conditions0.4460.0060.455
check.design0.4340.0050.442
checkClusterability3.7232.6306.543
classic1wayAnova0.0000.0000.001
compareNormalizationD_HC0.1750.0670.241
compute.selection.table0.7850.1600.949
compute_t_tests1.2500.2071.457
corrMatrixD_HC0.5250.0760.602
createMSnset1.9770.0952.088
createMSnset21.9690.1012.087
dapar_hc_ExportMenu0.1560.1740.332
dapar_hc_chart0.0700.0590.129
deleteLinesFromIndices0.5070.0200.529
densityPlotD_HC3.6171.6495.276
diffAnaComputeAdjustedPValues0.2360.0360.274
diffAnaComputeFDR000
diffAnaGetSignificant0.3080.0600.367
diffAnaSave0.3010.0560.357
diffAnaVolcanoplot0.1890.0260.216
diffAnaVolcanoplot_rCharts0.4200.1340.555
display.CC.visNet1.8080.0831.896
enrich_GO5.0300.6185.695
finalizeAggregation0.0010.0010.000
findMECBlock0.5000.0150.519
formatHSDResults0.0000.0000.001
formatLimmaResult0.1940.0260.220
formatPHResults000
formatPHTResults0.0000.0000.001
fudge2LRT000
get.pep.prot.cc1.6830.0311.724
getDesignLevel0.4470.0070.458
getIndicesConditions0.4380.0050.445
getIndicesOfLinesToRemove0.4870.0140.505
getListNbValuesInLines0.4200.0060.428
getNumberOf0.4810.0120.495
getNumberOfEmptyLines0.4830.0100.495
getPourcentageOfMV0.4870.0130.503
getProcessingInfo0.4240.0050.430
getProteinsStats0.4830.0150.502
getQuantile4Imp0.1070.0030.109
getTextForAggregation0.0010.0000.000
getTextForAnaDiff0.0010.0000.001
getTextForFiltering0.0000.0010.001
getTextForGOAnalysis000
getTextForHypothesisTest000
getTextForNewDataset0.0020.0000.003
getTextForNormalization0.0000.0000.001
getTextForpeptideImputation0.0010.0000.000
getTextForproteinImputation0.0000.0010.001
globalAdjPval0.4700.0550.527
group_GO5.3060.7706.174
hc_logFC_DensityPlot0.9240.4191.342
hc_mvTypePlot21.1930.3901.583
heatmapD0.7660.0730.849
heatmapForMissingValues0.2250.0290.256
histPValue_HC0.2850.1000.392
impute.pa20.5690.0330.606
inner.aggregate.iter0.5360.0260.564
inner.aggregate.topn0.6580.0310.692
inner.mean0.5100.0170.530
inner.sum0.5430.0180.564
is.subset0.0010.0010.001
limmaCompleteTest1.7370.0751.825
listSheets000
make.contrast0.4760.0080.486
make.design.10.4980.0080.509
make.design.20.5130.0080.526
make.design.30.4860.0070.496
make.design0.4380.0060.447
match.metacell0.5000.0160.518
metacell.def0.0060.0030.009
metacellHisto_HC0.5860.0750.666
metacellPerLinesHistoPerCondition_HC0.6980.1410.844
metacellPerLinesHisto_HC0.8450.3341.190
metacombine0.2150.0180.234
mvImage2.4130.1882.626
my_hc_ExportMenu0.1700.1870.362
my_hc_chart0.1680.1790.350
nonzero0.0540.0030.057
normalizeMethods.dapar0.0000.0000.001
pepa.test0.5260.0140.545
pkgs.require0.0000.0000.001
plotJitter1.8460.0561.912
plotJitter_rCharts1.7550.0941.858
plotPCA_Eigen0.5700.0450.618
plotPCA_Eigen_hc0.4720.0050.481
plotPCA_Ind0.4660.0070.476
plotPCA_Var0.4680.0050.475
postHocTest0.0000.0000.001
proportionConRev_HC0.0530.0570.111
rbindMSnset0.5550.0410.598
reIntroduceMEC0.5330.0260.562
readExcel000
removeLines0.5120.0240.537
samLRT000
saveParameters0.4630.0070.474
scatterplotEnrichGO_HC5.1390.6735.874
search.metacell.tags0.0080.0020.011
separateAdjPval0.1950.0150.211
splitAdjacencyMat0.4950.0150.513
test.design0.4970.0070.507
testAnovaModels0.1530.0140.171
thresholdpval4fdr0.0000.0010.000
translatedRandomBeta0.0020.0060.008
univ_AnnotDbPkg0.2420.0650.310
violinPlotD0.3580.0330.394
visualizeClusters1.6520.2661.926
vsn0.7310.0180.754
wrapper.CVDistD_HC2.3561.1003.439
wrapper.compareNormalizationD_HC62.76230.59392.969
wrapper.corrMatrixD_HC0.5940.0910.695
wrapper.dapar.impute.mi15.247 1.27516.960
wrapper.heatmapD0.7260.0490.778
wrapper.impute.KNN0.5250.0220.571
wrapper.impute.detQuant0.5320.0400.699
wrapper.impute.fixedValue0.5010.0450.711
wrapper.impute.mle0.4970.0310.658
wrapper.impute.pa0.1840.0290.257
wrapper.impute.pa20.6050.0370.645
wrapper.impute.slsa0.6760.0480.725
wrapper.mvImage0.2180.0350.281
wrapper.normalizeD0.4820.0160.541
wrapper.pca0.2040.0270.230
wrapperCalibrationPlot0.2340.0340.270
wrapperClassic1wayAnova000
wrapperRunClustering3.8850.4884.377
write.excel1.0350.1991.259
writeMSnsetToCSV0.4770.0240.520
writeMSnsetToExcel1.2130.3171.563