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This page was generated on 2025-09-26 12:04 -0400 (Fri, 26 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" 4619
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4563
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4563
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: 2025-09-25 13:45 -0400 (Thu, 25 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: 2025-09-25 20:31:59 -0400 (Thu, 25 Sep 2025)
EndedAt: 2025-09-25 20:42:54 -0400 (Thu, 25 Sep 2025)
EllapsedTime: 655.5 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 63.309 30.715  93.803
wrapper.dapar.impute.mi          15.486  1.367  17.623
barplotEnrichGO_HC                9.742  2.024  11.903
barplotGroupGO_HC                 5.232  0.993   6.415
group_GO                          5.357  0.749   6.172
checkClusterability               3.630  2.295   5.878
enrich_GO                         5.091  0.692   5.885
scatterplotEnrichGO_HC            5.015  0.631   5.699
densityPlotD_HC                   3.693  1.625   5.304
* 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 
 38.640   1.737  40.665 

Example timings

DAPAR.Rcheck/DAPAR-Ex.timings

nameusersystemelapsed
AggregateMetacell0.6190.0210.645
BuildAdjacencyMatrix0.4560.0070.464
BuildColumnToProteinDataset0.5560.0090.568
BuildMetaCell0.7750.0310.815
CVDistD_HC3.2770.1393.449
Children0.0040.0010.004
CountPep0.5080.0050.516
ExtendPalette0.0250.0010.026
GOAnalysisSave0.0010.0000.001
GetCC2.5470.0222.579
GetColorsForConditions0.4970.0080.512
GetDetailedNbPeptides0.4440.0050.451
GetDetailedNbPeptidesUsed000
GetIndices_BasedOnConditions0.4860.0060.497
GetIndices_MetacellFiltering0.4590.0050.468
GetIndices_WholeLine0.4360.0050.443
GetIndices_WholeMatrix0.4170.0050.423
GetKeyId0.4130.0050.419
GetMatAdj0.4860.0060.497
GetMetacell000
GetMetacellTags0.4620.0060.472
GetNbPeptidesUsed0.4500.0060.459
GetNbTags000
GetSoftAvailables0.0000.0000.001
GetTypeofData0.4230.0060.432
Get_AllComparisons0.2910.0140.306
GlobalQuantileAlignment0.4480.0050.453
GraphPepProt0.4700.0060.478
LH00.0000.0010.000
LH0.lm000
LH1000
LH1.lm0.0000.0000.001
LOESS1.1700.0151.193
MeanCentering1.2850.0251.320
MetaCellFiltering0.6100.0060.620
MetacellFilteringScope0.0010.0000.000
Metacell_DIA_NN0.5490.0150.571
Metacell_generic0.4940.0130.511
Metacell_maxquant0.5690.0200.594
Metacell_proline0.5200.0120.535
NumericalFiltering0.5260.0070.539
NumericalgetIndicesOfLinesToRemove0.4960.0070.511
OWAnova0.0060.0000.007
QuantileCentering0.4820.0060.490
SetCC2.3890.0232.424
SetMatAdj0.5330.0050.539
Set_POV_MEC_tags0.5020.0060.514
StringBasedFiltering0.5390.0070.554
StringBasedFiltering20.5380.0050.545
SumByColumns1.3680.0741.452
SymFilteringOperators000
UpdateMetacellAfterImputation0.4840.0050.493
aggregateIter0.6750.0080.692
aggregateIterParallel000
aggregateMean0.5800.0070.591
aggregateSum0.5890.0060.598
aggregateTopn0.5350.0080.550
applyAnovasOnProteins0.1340.0030.139
averageIntensities0.6940.1500.853
barplotEnrichGO_HC 9.742 2.02411.903
barplotGroupGO_HC5.2320.9936.415
boxPlotD_HC0.2990.0970.396
buildGraph1.7430.0441.795
check.conditions0.4320.0050.439
check.design0.4180.0060.428
checkClusterability3.6302.2955.878
classic1wayAnova0.0000.0000.001
compareNormalizationD_HC0.1730.0650.240
compute.selection.table0.7700.1650.945
compute_t_tests1.2440.2161.467
corrMatrixD_HC0.5630.0790.646
createMSnset2.0740.1052.191
createMSnset22.0530.1012.171
dapar_hc_ExportMenu0.1670.1710.341
dapar_hc_chart0.0680.0560.125
deleteLinesFromIndices0.5130.0190.533
densityPlotD_HC3.6931.6255.304
diffAnaComputeAdjustedPValues0.2370.0370.274
diffAnaComputeFDR0.0000.0000.001
diffAnaGetSignificant0.3310.0640.395
diffAnaSave0.3010.0560.356
diffAnaVolcanoplot0.2140.0260.242
diffAnaVolcanoplot_rCharts0.4460.1340.581
display.CC.visNet1.7760.0881.871
enrich_GO5.0910.6925.885
finalizeAggregation0.0000.0000.001
findMECBlock0.4890.0150.506
formatHSDResults000
formatLimmaResult0.1830.0240.209
formatPHResults0.0000.0010.000
formatPHTResults0.0000.0010.001
fudge2LRT000
get.pep.prot.cc1.6770.0321.715
getDesignLevel0.4580.0060.468
getIndicesConditions0.4370.0070.446
getIndicesOfLinesToRemove0.4800.0170.515
getListNbValuesInLines0.4170.0060.425
getNumberOf0.4770.0150.496
getNumberOfEmptyLines0.4540.0090.467
getPourcentageOfMV0.4620.0150.478
getProcessingInfo0.4770.0060.485
getProteinsStats0.4820.0160.501
getQuantile4Imp0.1050.0030.109
getTextForAggregation0.0000.0010.001
getTextForAnaDiff000
getTextForFiltering000
getTextForGOAnalysis0.0010.0000.001
getTextForHypothesisTest0.0000.0010.001
getTextForNewDataset0.0020.0010.003
getTextForNormalization0.0000.0000.001
getTextForpeptideImputation000
getTextForproteinImputation0.0010.0000.001
globalAdjPval0.4910.0620.558
group_GO5.3570.7496.172
hc_logFC_DensityPlot0.9500.4311.379
hc_mvTypePlot21.2020.3951.593
heatmapD0.7910.0720.869
heatmapForMissingValues0.2240.0310.256
histPValue_HC0.3100.1080.437
impute.pa20.5510.0320.586
inner.aggregate.iter0.5400.0250.568
inner.aggregate.topn0.6450.0270.677
inner.mean0.5120.0170.534
inner.sum0.5010.0170.522
is.subset0.0010.0010.001
limmaCompleteTest1.7240.0751.808
listSheets000
make.contrast0.4850.0070.495
make.design.10.4940.0080.510
make.design.20.4560.0060.464
make.design.30.4830.0080.494
make.design0.4770.0070.487
match.metacell0.5160.0140.533
metacell.def0.0060.0030.008
metacellHisto_HC0.5720.0730.649
metacellPerLinesHistoPerCondition_HC0.6870.1320.823
metacellPerLinesHisto_HC0.8700.3311.214
metacombine0.2080.0150.225
mvImage2.3630.1762.556
my_hc_ExportMenu0.1660.1770.350
my_hc_chart0.1690.1720.346
nonzero0.0630.0040.069
normalizeMethods.dapar0.0000.0000.001
pepa.test0.5160.0150.533
pkgs.require000
plotJitter1.7970.0471.853
plotJitter_rCharts1.7150.0941.817
plotPCA_Eigen0.5610.0480.615
plotPCA_Eigen_hc0.4610.0060.470
plotPCA_Ind0.4480.0080.460
plotPCA_Var0.4520.0070.465
postHocTest000
proportionConRev_HC0.0610.0630.126
rbindMSnset0.5860.0380.627
reIntroduceMEC0.5630.0280.593
readExcel000
removeLines0.5210.0240.548
samLRT000
saveParameters0.4560.0070.465
scatterplotEnrichGO_HC5.0150.6315.699
search.metacell.tags0.0090.0030.013
separateAdjPval0.2040.0150.220
splitAdjacencyMat0.5070.0150.527
test.design0.5120.0070.521
testAnovaModels0.1540.0140.167
thresholdpval4fdr0.0000.0010.000
translatedRandomBeta0.0030.0150.018
univ_AnnotDbPkg0.2300.1110.344
violinPlotD0.3720.0310.410
visualizeClusters1.6140.2451.861
vsn0.7220.0200.747
wrapper.CVDistD_HC2.4051.1053.482
wrapper.compareNormalizationD_HC63.30930.71593.803
wrapper.corrMatrixD_HC0.5390.1170.920
wrapper.dapar.impute.mi15.486 1.36717.623
wrapper.heatmapD0.6980.0741.065
wrapper.impute.KNN0.5160.0260.616
wrapper.impute.detQuant0.5910.0400.641
wrapper.impute.fixedValue0.5950.0370.632
wrapper.impute.mle0.5310.0220.557
wrapper.impute.pa0.1760.0230.228
wrapper.impute.pa20.5890.0500.738
wrapper.impute.slsa0.6520.0480.748
wrapper.mvImage0.2000.0260.232
wrapper.normalizeD0.4580.0280.660
wrapper.pca0.1930.0290.224
wrapperCalibrationPlot0.2260.0360.266
wrapperClassic1wayAnova0.0010.0000.000
wrapperRunClustering3.9920.5594.665
write.excel1.0530.2011.278
writeMSnsetToCSV0.5020.0240.547
writeMSnsetToExcel1.2780.2931.599