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This page was generated on 2025-09-23 12:04 -0400 (Tue, 23 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4816
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4605
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4549
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: 2025-09-22 13:45 -0400 (Mon, 22 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: 2025-09-22 20:25:31 -0400 (Mon, 22 Sep 2025)
EndedAt: 2025-09-22 20:36:19 -0400 (Mon, 22 Sep 2025)
EllapsedTime: 648.1 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 63.419 30.975  94.217
wrapper.dapar.impute.mi          14.958  1.280  16.936
barplotEnrichGO_HC                9.668  1.956  11.777
group_GO                          5.281  0.715   6.068
barplotGroupGO_HC                 5.197  0.724   5.967
checkClusterability               3.606  2.289   5.837
scatterplotEnrichGO_HC            5.129  0.664   5.860
enrich_GO                         5.155  0.632   5.819
densityPlotD_HC                   3.668  1.689   5.360
* 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 18 | SKIP 0 | PASS 66 ]

[ FAIL 0 | WARN 18 | SKIP 0 | PASS 66 ]
> 
> proc.time()
   user  system elapsed 
 36.469   1.831  43.488 

Example timings

DAPAR.Rcheck/DAPAR-Ex.timings

nameusersystemelapsed
AggregateMetacell0.6160.0210.641
BuildAdjacencyMatrix0.4810.0060.490
BuildColumnToProteinDataset0.5770.0080.591
BuildMetaCell0.7450.0340.783
CVDistD_HC3.2390.1333.394
Children0.0050.0010.005
CountPep0.5020.0050.507
ExtendPalette0.0270.0010.029
GOAnalysisSave000
GetCC2.5790.0192.608
GetColorsForConditions0.4640.0040.469
GetDetailedNbPeptides0.4740.0050.480
GetDetailedNbPeptidesUsed0.0000.0010.000
GetIndices_BasedOnConditions0.4600.0050.467
GetIndices_MetacellFiltering0.4800.0050.488
GetIndices_WholeLine0.4870.0050.494
GetIndices_WholeMatrix0.4780.0060.487
GetKeyId0.4520.0050.458
GetMatAdj0.5170.0060.525
GetMetacell000
GetMetacellTags0.4280.0050.434
GetNbPeptidesUsed0.4380.0060.447
GetNbTags000
GetSoftAvailables0.0000.0000.001
GetTypeofData0.4320.0060.440
Get_AllComparisons0.2730.0190.293
GlobalQuantileAlignment0.4680.0040.474
GraphPepProt0.4750.0050.481
LH00.0000.0000.001
LH0.lm000
LH1000
LH1.lm000
LOESS1.1660.0141.184
MeanCentering1.3410.0251.372
MetaCellFiltering0.6500.0090.666
MetacellFilteringScope0.0000.0000.001
Metacell_DIA_NN0.5480.0120.564
Metacell_generic0.5290.0120.545
Metacell_maxquant0.5600.0220.587
Metacell_proline0.5160.0110.531
NumericalFiltering0.5180.0060.528
NumericalgetIndicesOfLinesToRemove0.5030.0050.511
OWAnova0.0060.0000.005
QuantileCentering0.4810.0050.492
SetCC2.3730.0222.407
SetMatAdj0.5030.0050.513
Set_POV_MEC_tags0.4820.0060.492
StringBasedFiltering0.5370.0090.554
StringBasedFiltering20.5320.0070.546
SumByColumns1.4090.0791.499
SymFilteringOperators000
UpdateMetacellAfterImputation0.5040.0070.517
aggregateIter0.6100.0080.625
aggregateIterParallel000
aggregateMean0.5840.0070.598
aggregateSum0.6010.0070.614
aggregateTopn0.5830.0070.595
applyAnovasOnProteins0.1270.0040.131
averageIntensities0.6070.1330.744
barplotEnrichGO_HC 9.668 1.95611.777
barplotGroupGO_HC5.1970.7245.967
boxPlotD_HC0.2930.1030.399
buildGraph1.6730.0441.721
check.conditions0.4600.0610.578
check.design0.4520.0460.537
checkClusterability3.6062.2895.837
classic1wayAnova000
compareNormalizationD_HC0.1660.0650.234
compute.selection.table0.7970.1710.974
compute_t_tests1.2000.1981.395
corrMatrixD_HC0.5340.0780.613
createMSnset2.0190.0962.125
createMSnset22.0270.0952.130
dapar_hc_ExportMenu0.1580.1760.340
dapar_hc_chart0.0690.0590.130
deleteLinesFromIndices0.5210.0210.544
densityPlotD_HC3.6681.6895.360
diffAnaComputeAdjustedPValues0.2530.0390.292
diffAnaComputeFDR0.0000.0010.000
diffAnaGetSignificant0.3270.0600.385
diffAnaSave0.3030.0550.356
diffAnaVolcanoplot0.2000.0270.228
diffAnaVolcanoplot_rCharts0.4250.1330.556
display.CC.visNet1.8270.0921.927
enrich_GO5.1550.6325.819
finalizeAggregation0.0000.0010.000
findMECBlock0.5030.0130.519
formatHSDResults0.0000.0000.001
formatLimmaResult0.1910.0260.217
formatPHResults0.0010.0010.000
formatPHTResults000
fudge2LRT000
get.pep.prot.cc1.7360.0331.778
getDesignLevel0.4380.0050.446
getIndicesConditions0.4160.0060.424
getIndicesOfLinesToRemove0.4610.0130.476
getListNbValuesInLines0.4180.0050.425
getNumberOf0.4560.0130.471
getNumberOfEmptyLines0.4730.0100.487
getPourcentageOfMV0.4900.0170.510
getProcessingInfo0.4690.0070.478
getProteinsStats0.5000.0190.522
getQuantile4Imp0.1130.0030.117
getTextForAggregation000
getTextForAnaDiff000
getTextForFiltering000
getTextForGOAnalysis0.0010.0000.000
getTextForHypothesisTest000
getTextForNewDataset0.0020.0000.003
getTextForNormalization0.0010.0000.000
getTextForpeptideImputation0.0010.0000.001
getTextForproteinImputation000
globalAdjPval0.5100.0660.579
group_GO5.2810.7156.068
hc_logFC_DensityPlot0.9730.4251.392
hc_mvTypePlot21.1910.3921.577
heatmapD0.7620.0600.830
heatmapForMissingValues0.2170.0260.245
histPValue_HC0.2980.1070.409
impute.pa20.5750.0310.609
inner.aggregate.iter0.5870.0310.627
inner.aggregate.topn0.6690.0300.703
inner.mean0.5350.0180.556
inner.sum0.5400.0190.566
is.subset0.0000.0010.001
limmaCompleteTest1.7640.0761.856
listSheets000
make.contrast0.5220.0080.534
make.design.10.4960.0080.507
make.design.20.5240.0080.536
make.design.30.5230.0110.544
make.design0.5290.0100.545
match.metacell0.5450.0170.564
metacell.def0.0060.0030.010
metacellHisto_HC0.6010.0890.701
metacellPerLinesHistoPerCondition_HC0.6970.1450.861
metacellPerLinesHisto_HC0.8380.3161.157
metacombine0.1830.0150.199
mvImage2.3830.1722.567
my_hc_ExportMenu0.1620.1800.343
my_hc_chart0.1700.1800.356
nonzero0.0600.0020.063
normalizeMethods.dapar0.0000.0000.001
pepa.test0.5300.0150.548
pkgs.require0.0000.0000.001
plotJitter1.7150.0501.780
plotJitter_rCharts1.7050.0991.813
plotPCA_Eigen0.5920.0460.640
plotPCA_Eigen_hc0.4660.0060.478
plotPCA_Ind0.4600.0080.471
plotPCA_Var0.4580.0070.470
postHocTest0.0000.0010.001
proportionConRev_HC0.0640.0660.131
rbindMSnset0.5990.0440.647
reIntroduceMEC0.4930.0280.525
readExcel0.0000.0000.001
removeLines0.5200.0250.550
samLRT0.0010.0000.000
saveParameters0.4520.0070.466
scatterplotEnrichGO_HC5.1290.6645.860
search.metacell.tags0.0090.0030.012
separateAdjPval0.2010.0130.214
splitAdjacencyMat0.4980.0140.516
test.design0.4650.0070.474
testAnovaModels0.1510.0130.166
thresholdpval4fdr000
translatedRandomBeta0.0020.0110.014
univ_AnnotDbPkg0.2400.0860.328
violinPlotD0.3620.0330.397
visualizeClusters1.6340.2521.892
vsn0.7220.0180.744
wrapper.CVDistD_HC2.3941.1013.472
wrapper.compareNormalizationD_HC63.41930.97594.217
wrapper.corrMatrixD_HC0.5740.0920.696
wrapper.dapar.impute.mi14.958 1.28016.936
wrapper.heatmapD0.7220.0640.854
wrapper.impute.KNN0.5370.0220.561
wrapper.impute.detQuant0.6020.0380.647
wrapper.impute.fixedValue0.5940.0460.670
wrapper.impute.mle0.5650.0240.595
wrapper.impute.pa0.1750.0220.201
wrapper.impute.pa20.6270.0410.673
wrapper.impute.slsa0.7010.0470.749
wrapper.mvImage0.2010.0290.230
wrapper.normalizeD0.5010.0100.518
wrapper.pca0.2040.0290.236
wrapperCalibrationPlot0.2400.0310.271
wrapperClassic1wayAnova000
wrapperRunClustering3.9530.4914.470
write.excel1.0490.1821.243
writeMSnsetToCSV0.5150.0220.556
writeMSnsetToExcel1.2630.2621.541