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This page was generated on 2025-09-20 12:04 -0400 (Sat, 20 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4814
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4603
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4547
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4553
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 516/2333HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DAPAR 1.41.0  (landing page)
Samuel Wieczorek
Snapshot Date: 2025-09-19 13:45 -0400 (Fri, 19 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: 2025-09-19 20:22:23 -0400 (Fri, 19 Sep 2025)
EndedAt: 2025-09-19 20:33:11 -0400 (Fri, 19 Sep 2025)
EllapsedTime: 647.8 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 63.558 30.721  93.851
wrapper.dapar.impute.mi          15.456  1.301  16.951
barplotEnrichGO_HC                9.369  2.049  11.643
checkClusterability               3.841  2.402   6.185
enrich_GO                         5.410  0.756   6.225
group_GO                          5.338  0.733   6.154
barplotGroupGO_HC                 5.179  0.715   5.943
scatterplotEnrichGO_HC            5.073  0.638   5.768
densityPlotD_HC                   3.474  1.572   5.022
* 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 
 37.981   1.681  43.161 

Example timings

DAPAR.Rcheck/DAPAR-Ex.timings

nameusersystemelapsed
AggregateMetacell0.5990.0180.622
BuildAdjacencyMatrix0.4690.0050.476
BuildColumnToProteinDataset0.5560.0080.568
BuildMetaCell0.7530.0330.792
CVDistD_HC3.1290.1283.280
Children0.0060.0010.006
CountPep0.5040.0060.511
ExtendPalette0.0310.0010.033
GOAnalysisSave000
GetCC2.6710.0222.702
GetColorsForConditions0.4910.0090.509
GetDetailedNbPeptides0.4770.0050.484
GetDetailedNbPeptidesUsed000
GetIndices_BasedOnConditions0.4770.0060.486
GetIndices_MetacellFiltering0.4840.0070.498
GetIndices_WholeLine0.4730.0070.482
GetIndices_WholeMatrix0.4570.0060.464
GetKeyId0.4700.0080.481
GetMatAdj0.5390.0100.553
GetMetacell0.0000.0010.000
GetMetacellTags0.4920.0070.502
GetNbPeptidesUsed0.4810.0080.492
GetNbTags000
GetSoftAvailables0.0010.0000.001
GetTypeofData0.4950.0060.502
Get_AllComparisons0.3060.0160.326
GlobalQuantileAlignment0.5120.0060.520
GraphPepProt0.4920.0070.504
LH00.0000.0000.001
LH0.lm000
LH1000
LH1.lm000
LOESS1.1960.0161.219
MeanCentering1.3400.0201.367
MetaCellFiltering0.6420.0070.652
MetacellFilteringScope000
Metacell_DIA_NN0.5170.0110.531
Metacell_generic0.5240.0120.538
Metacell_maxquant0.5770.0230.605
Metacell_proline0.5400.0110.554
NumericalFiltering0.5310.0060.541
NumericalgetIndicesOfLinesToRemove0.4950.0050.505
OWAnova0.0080.0000.008
QuantileCentering0.4820.0040.488
SetCC2.3470.0282.391
SetMatAdj0.5540.0090.568
Set_POV_MEC_tags0.4250.0060.434
StringBasedFiltering0.4570.0060.465
StringBasedFiltering20.4980.0060.506
SumByColumns1.4200.0781.507
SymFilteringOperators000
UpdateMetacellAfterImputation0.4920.0070.504
aggregateIter0.6860.0090.701
aggregateIterParallel0.0010.0000.001
aggregateMean0.5920.0090.605
aggregateSum0.6240.0090.638
aggregateTopn0.5960.0080.610
applyAnovasOnProteins0.1450.0040.150
averageIntensities0.6950.1490.849
barplotEnrichGO_HC 9.369 2.04911.643
barplotGroupGO_HC5.1790.7155.943
boxPlotD_HC0.2930.0960.388
buildGraph1.6940.0451.747
check.conditions0.4470.0070.456
check.design0.4390.0070.449
checkClusterability3.8412.4026.185
classic1wayAnova000
compareNormalizationD_HC0.1820.0640.246
compute.selection.table0.7960.1690.969
compute_t_tests1.2590.2091.469
corrMatrixD_HC0.5550.0860.650
createMSnset1.9880.1032.103
createMSnset22.0750.0942.181
dapar_hc_ExportMenu0.1560.1690.327
dapar_hc_chart0.0750.0590.135
deleteLinesFromIndices0.4910.0200.514
densityPlotD_HC3.4741.5725.022
diffAnaComputeAdjustedPValues0.2650.0470.314
diffAnaComputeFDR000
diffAnaGetSignificant0.3770.0830.460
diffAnaSave0.3450.0740.420
diffAnaVolcanoplot0.2180.0340.253
diffAnaVolcanoplot_rCharts0.4930.1620.657
display.CC.visNet1.9050.1222.051
enrich_GO5.4100.7566.225
finalizeAggregation000
findMECBlock0.5200.0170.545
formatHSDResults000
formatLimmaResult0.1960.0260.223
formatPHResults0.0000.0000.001
formatPHTResults0.0000.0000.001
fudge2LRT000
get.pep.prot.cc1.6850.0341.725
getDesignLevel0.4630.0060.471
getIndicesConditions0.4700.0070.480
getIndicesOfLinesToRemove0.4620.0160.485
getListNbValuesInLines0.4560.0070.467
getNumberOf0.4650.0140.481
getNumberOfEmptyLines0.4870.0100.503
getPourcentageOfMV0.4950.0160.514
getProcessingInfo0.4650.0060.473
getProteinsStats0.5160.0170.535
getQuantile4Imp0.1130.0030.117
getTextForAggregation000
getTextForAnaDiff0.0010.0000.001
getTextForFiltering0.0010.0000.000
getTextForGOAnalysis0.0010.0000.000
getTextForHypothesisTest0.0000.0000.001
getTextForNewDataset0.0030.0000.003
getTextForNormalization0.0000.0000.001
getTextForpeptideImputation0.0000.0000.001
getTextForproteinImputation0.0000.0000.001
globalAdjPval0.4980.0630.569
group_GO5.3380.7336.154
hc_logFC_DensityPlot0.8350.3531.186
hc_mvTypePlot21.1540.3531.508
heatmapD0.7800.0670.856
heatmapForMissingValues0.2120.0240.238
histPValue_HC0.2750.0920.372
impute.pa20.5470.0280.581
inner.aggregate.iter0.5310.0210.554
inner.aggregate.topn0.5850.0270.615
inner.mean0.5010.0150.519
inner.sum0.4780.0140.495
is.subset0.0010.0000.001
limmaCompleteTest1.5720.0671.651
listSheets0.0000.0000.001
make.contrast0.4710.0070.480
make.design.10.4840.0060.494
make.design.20.4740.0060.484
make.design.30.4750.0060.484
make.design0.4620.0060.472
match.metacell0.5070.0160.527
metacell.def0.0070.0030.010
metacellHisto_HC0.5800.0710.655
metacellPerLinesHistoPerCondition_HC0.6630.1270.794
metacellPerLinesHisto_HC0.8110.3191.137
metacombine0.2000.0150.215
mvImage2.3820.1762.573
my_hc_ExportMenu0.1580.1770.345
my_hc_chart0.1720.1820.361
nonzero0.0570.0030.061
normalizeMethods.dapar000
pepa.test0.5410.0140.558
pkgs.require0.0000.0010.000
plotJitter1.7850.0491.849
plotJitter_rCharts1.5890.0841.680
plotPCA_Eigen0.4920.0430.538
plotPCA_Eigen_hc0.3870.0040.392
plotPCA_Ind0.4120.0070.422
plotPCA_Var0.3850.0040.391
postHocTest000
proportionConRev_HC0.0460.0530.098
rbindMSnset0.5110.0320.543
reIntroduceMEC0.4920.0280.524
readExcel000
removeLines0.5050.0230.532
samLRT000
saveParameters0.4040.0050.410
scatterplotEnrichGO_HC5.0730.6385.768
search.metacell.tags0.0070.0020.009
separateAdjPval0.1870.0140.201
splitAdjacencyMat0.5220.0140.541
test.design0.4830.0070.496
testAnovaModels0.1420.0130.156
thresholdpval4fdr000
translatedRandomBeta0.0020.0100.013
univ_AnnotDbPkg0.2380.0820.322
violinPlotD0.3710.0340.408
visualizeClusters1.6850.2571.944
vsn0.7930.0220.821
wrapper.CVDistD_HC2.5651.1913.744
wrapper.compareNormalizationD_HC63.55830.72193.851
wrapper.corrMatrixD_HC0.5610.0990.713
wrapper.dapar.impute.mi15.456 1.30116.951
wrapper.heatmapD0.7760.0490.833
wrapper.impute.KNN0.5680.0190.589
wrapper.impute.detQuant0.6160.0370.659
wrapper.impute.fixedValue0.6020.0370.643
wrapper.impute.mle0.5400.0280.579
wrapper.impute.pa0.1760.0210.199
wrapper.impute.pa20.6050.0320.638
wrapper.impute.slsa0.6860.0480.738
wrapper.mvImage0.2120.0270.241
wrapper.normalizeD0.4820.0100.504
wrapper.pca0.2010.0270.230
wrapperCalibrationPlot0.2330.0300.264
wrapperClassic1wayAnova000
wrapperRunClustering3.8710.4994.386
write.excel1.0690.1821.267
writeMSnsetToCSV0.4900.0200.528
writeMSnsetToExcel1.2240.2761.518