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This page was generated on 2025-09-25 12:05 -0400 (Thu, 25 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4831
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4618
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4562
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: 2025-09-24 13:45 -0400 (Wed, 24 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: 2025-09-24 20:30:15 -0400 (Wed, 24 Sep 2025)
EndedAt: 2025-09-24 20:41:07 -0400 (Wed, 24 Sep 2025)
EllapsedTime: 651.9 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 63.039 30.576  93.807
wrapper.dapar.impute.mi          15.256  1.309  17.191
barplotEnrichGO_HC               10.261  2.284  12.784
checkClusterability               4.157  2.951   7.230
barplotGroupGO_HC                 5.488  0.956   6.756
group_GO                          5.434  0.766   6.327
enrich_GO                         5.186  0.648   5.889
scatterplotEnrichGO_HC            5.159  0.645   5.874
densityPlotD_HC                   3.724  1.653   5.366
* 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 
 37.130   1.757  39.279 

Example timings

DAPAR.Rcheck/DAPAR-Ex.timings

nameusersystemelapsed
AggregateMetacell0.6030.0190.626
BuildAdjacencyMatrix0.4480.0060.455
BuildColumnToProteinDataset0.5690.0080.580
BuildMetaCell0.7630.0300.799
CVDistD_HC3.1650.1313.326
Children0.0070.0000.007
CountPep0.4910.0060.499
ExtendPalette0.0260.0020.028
GOAnalysisSave000
GetCC2.4870.0212.518
GetColorsForConditions0.4420.0050.449
GetDetailedNbPeptides0.4540.0040.459
GetDetailedNbPeptidesUsed000
GetIndices_BasedOnConditions0.4720.0050.480
GetIndices_MetacellFiltering0.4590.0060.472
GetIndices_WholeLine0.4620.0060.471
GetIndices_WholeMatrix0.4650.0060.473
GetKeyId0.4370.0060.448
GetMatAdj0.5170.0070.530
GetMetacell0.0010.0000.000
GetMetacellTags0.4640.0070.476
GetNbPeptidesUsed0.4710.0080.485
GetNbTags000
GetSoftAvailables0.0010.0000.000
GetTypeofData0.4760.0070.484
Get_AllComparisons0.3020.0170.402
GlobalQuantileAlignment0.4710.0060.486
GraphPepProt0.4770.0060.496
LH0000
LH0.lm0.0000.0000.001
LH10.0000.0010.000
LH1.lm0.0000.0000.001
LOESS1.2290.0201.255
MeanCentering1.3660.0281.404
MetaCellFiltering0.6640.0090.685
MetacellFilteringScope0.0000.0000.001
Metacell_DIA_NN0.5510.0170.575
Metacell_generic0.5650.0160.592
Metacell_maxquant0.6340.0290.672
Metacell_proline0.5410.0130.563
NumericalFiltering0.5500.0070.561
NumericalgetIndicesOfLinesToRemove0.5140.0060.522
OWAnova0.0060.0010.007
QuantileCentering0.4810.0070.494
SetCC2.2930.0272.337
SetMatAdj0.5190.0060.529
Set_POV_MEC_tags0.4880.0060.494
StringBasedFiltering0.5090.0070.518
StringBasedFiltering20.4930.0060.503
SumByColumns1.3570.0761.441
SymFilteringOperators0.0000.0000.001
UpdateMetacellAfterImputation0.4770.0060.486
aggregateIter0.6460.0070.658
aggregateIterParallel000
aggregateMean0.5550.0070.565
aggregateSum0.5700.0070.596
aggregateTopn0.5410.0080.553
applyAnovasOnProteins0.1550.0040.160
averageIntensities0.7540.1960.986
barplotEnrichGO_HC10.261 2.28412.784
barplotGroupGO_HC5.4880.9566.756
boxPlotD_HC0.2860.1100.404
buildGraph1.7940.0451.849
check.conditions0.4410.0060.450
check.design0.4590.0060.469
checkClusterability4.1572.9517.230
classic1wayAnova000
compareNormalizationD_HC0.1800.0910.274
compute.selection.table0.8270.1741.021
compute_t_tests1.2660.2221.490
corrMatrixD_HC0.5600.0760.637
createMSnset1.9890.0892.086
createMSnset21.9030.0932.002
dapar_hc_ExportMenu0.1540.1640.320
dapar_hc_chart0.0700.0540.124
deleteLinesFromIndices0.5150.0190.539
densityPlotD_HC3.7241.6535.366
diffAnaComputeAdjustedPValues0.2460.0390.287
diffAnaComputeFDR000
diffAnaGetSignificant0.3250.0660.392
diffAnaSave0.3070.0610.371
diffAnaVolcanoplot0.2040.0280.233
diffAnaVolcanoplot_rCharts0.4520.1380.592
display.CC.visNet1.8510.0951.961
enrich_GO5.1860.6485.889
finalizeAggregation0.0010.0000.000
findMECBlock0.4950.0110.507
formatHSDResults0.0000.0000.001
formatLimmaResult0.1790.0250.204
formatPHResults000
formatPHTResults000
fudge2LRT0.0000.0000.001
get.pep.prot.cc1.6700.0251.701
getDesignLevel0.4320.0050.440
getIndicesConditions0.4590.0060.467
getIndicesOfLinesToRemove0.4570.0120.471
getListNbValuesInLines0.4430.0060.451
getNumberOf0.4920.0120.506
getNumberOfEmptyLines0.4660.0100.482
getPourcentageOfMV0.4580.0130.475
getProcessingInfo0.4360.0050.443
getProteinsStats0.4750.0140.490
getQuantile4Imp0.1080.0030.112
getTextForAggregation0.0000.0010.000
getTextForAnaDiff0.0000.0000.001
getTextForFiltering000
getTextForGOAnalysis0.0010.0000.001
getTextForHypothesisTest000
getTextForNewDataset0.0020.0000.003
getTextForNormalization0.0000.0000.001
getTextForpeptideImputation0.0000.0010.000
getTextForproteinImputation0.0000.0000.001
globalAdjPval0.4700.0540.528
group_GO5.4340.7666.327
hc_logFC_DensityPlot0.9220.4081.330
hc_mvTypePlot21.2480.3951.643
heatmapD0.7930.0740.893
heatmapForMissingValues0.2240.0320.258
histPValue_HC0.2990.1030.407
impute.pa20.5780.0320.614
inner.aggregate.iter0.5900.0320.635
inner.aggregate.topn0.6490.0280.679
inner.mean0.4870.0160.504
inner.sum0.5230.0190.567
is.subset0.0010.0000.001
limmaCompleteTest1.7540.0761.842
listSheets0.0010.0010.001
make.contrast0.4800.0060.488
make.design.10.4900.0090.504
make.design.20.4970.0070.508
make.design.30.4790.0070.487
make.design0.4960.0080.516
match.metacell0.4870.0150.512
metacell.def0.0060.0030.008
metacellHisto_HC0.6100.0900.725
metacellPerLinesHistoPerCondition_HC0.7310.1580.920
metacellPerLinesHisto_HC0.8870.3591.265
metacombine0.2130.0180.233
mvImage2.6160.1952.836
my_hc_ExportMenu0.1640.1740.339
my_hc_chart0.1670.1690.337
nonzero0.0610.0030.066
normalizeMethods.dapar000
pepa.test0.4870.0140.502
pkgs.require000
plotJitter1.7370.0501.795
plotJitter_rCharts1.6330.0971.738
plotPCA_Eigen0.5650.0520.626
plotPCA_Eigen_hc0.4340.0070.445
plotPCA_Ind0.4680.0090.483
plotPCA_Var0.4600.0060.470
postHocTest000
proportionConRev_HC0.0510.0570.111
rbindMSnset0.5670.0400.610
reIntroduceMEC0.5070.0270.537
readExcel000
removeLines0.4770.0210.499
samLRT0.0000.0000.001
saveParameters0.4340.0060.441
scatterplotEnrichGO_HC5.1590.6455.874
search.metacell.tags0.0090.0030.012
separateAdjPval0.1940.0130.210
splitAdjacencyMat0.5230.0160.544
test.design0.4500.0060.458
testAnovaModels0.1400.0130.157
thresholdpval4fdr000
translatedRandomBeta0.0020.0070.009
univ_AnnotDbPkg0.2350.0630.299
violinPlotD0.3480.0330.383
visualizeClusters1.6830.2621.953
vsn0.7450.0190.767
wrapper.CVDistD_HC2.4411.1383.565
wrapper.compareNormalizationD_HC63.03930.57693.807
wrapper.corrMatrixD_HC0.5900.0810.675
wrapper.dapar.impute.mi15.256 1.30917.191
wrapper.heatmapD0.7610.0841.169
wrapper.impute.KNN0.4320.0310.599
wrapper.impute.detQuant0.5000.0520.627
wrapper.impute.fixedValue0.6060.0430.667
wrapper.impute.mle0.5660.0220.590
wrapper.impute.pa0.1810.0210.202
wrapper.impute.pa20.6730.0380.712
wrapper.impute.slsa0.7460.0520.801
wrapper.mvImage0.2220.0320.259
wrapper.normalizeD0.5300.0080.539
wrapper.pca0.2130.0300.248
wrapperCalibrationPlot0.2510.0360.287
wrapperClassic1wayAnova000
wrapperRunClustering3.9870.5194.699
write.excel1.0960.2041.350
writeMSnsetToCSV0.4880.0240.526
writeMSnsetToExcel1.2420.2691.525