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This page was generated on 2025-10-02 12:07 -0400 (Thu, 02 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4844
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4631
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4576
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4576
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 517/2337HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DAPAR 1.41.0  (landing page)
Samuel Wieczorek
Snapshot Date: 2025-10-01 13:45 -0400 (Wed, 01 Oct 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 taishan

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: DAPAR
Version: 1.41.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:DAPAR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings DAPAR_1.41.0.tar.gz
StartedAt: 2025-09-30 07:29:39 -0000 (Tue, 30 Sep 2025)
EndedAt: 2025-09-30 07:40:35 -0000 (Tue, 30 Sep 2025)
EllapsedTime: 656.4 seconds
RetCode: 0
Status:   OK  
CheckDir: DAPAR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:DAPAR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings DAPAR_1.41.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/DAPAR.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* 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 loading without being on the library search path ... 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 57.047 15.572  74.992
wrapper.dapar.impute.mi          19.619  0.756  20.558
barplotEnrichGO_HC                8.660  1.523  10.359
barplotGroupGO_HC                 4.935  0.514   5.497
enrich_GO                         4.846  0.420   5.318
group_GO                          4.788  0.355   5.198
scatterplotEnrichGO_HC            4.674  0.329   5.054
checkClusterability               3.256  1.512   5.038
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking PDF version of manual ... OK
* DONE

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


Installation output

DAPAR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL DAPAR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0/site-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 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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 
 40.303   1.449  41.875 

Example timings

DAPAR.Rcheck/DAPAR-Ex.timings

nameusersystemelapsed
AggregateMetacell0.6250.0400.674
BuildAdjacencyMatrix0.4660.0240.491
BuildColumnToProteinDataset0.5830.0480.633
BuildMetaCell0.7310.1670.906
CVDistD_HC4.1040.4224.598
Children0.0060.0010.007
CountPep0.4700.0360.508
ExtendPalette0.0350.0040.039
GOAnalysisSave000
GetCC2.3670.2072.581
GetColorsForConditions0.4320.0130.446
GetDetailedNbPeptides0.4590.0070.466
GetDetailedNbPeptidesUsed000
GetIndices_BasedOnConditions0.4630.0040.469
GetIndices_MetacellFiltering0.4590.0080.469
GetIndices_WholeLine0.4370.0280.466
GetIndices_WholeMatrix0.4410.0160.459
GetKeyId0.4250.0040.430
GetMatAdj0.5100.0120.524
GetMetacell000
GetMetacellTags0.4540.0000.454
GetNbPeptidesUsed0.4500.0240.474
GetNbTags000
GetSoftAvailables000
GetTypeofData0.4180.0160.435
Get_AllComparisons0.3230.0270.354
GlobalQuantileAlignment0.4700.0000.474
GraphPepProt0.4670.0040.473
LH0000
LH0.lm000
LH1000
LH1.lm000
LOESS1.8290.0161.850
MeanCentering0.4710.0110.483
MetaCellFiltering0.6670.0080.677
MetacellFilteringScope000
Metacell_DIA_NN0.5150.0120.528
Metacell_generic0.4360.0040.440
Metacell_maxquant0.4780.0240.503
Metacell_proline0.4360.0040.442
NumericalFiltering0.4960.0040.502
NumericalgetIndicesOfLinesToRemove0.4470.0040.452
OWAnova0.0090.0000.009
QuantileCentering0.4620.0200.483
SetCC2.0520.1832.240
SetMatAdj0.4980.0000.500
Set_POV_MEC_tags0.4550.0040.461
StringBasedFiltering0.4860.0040.492
StringBasedFiltering20.4780.0040.483
SumByColumns1.7590.1631.927
SymFilteringOperators000
UpdateMetacellAfterImputation0.4630.0080.472
aggregateIter0.6340.0360.672
aggregateIterParallel000
aggregateMean0.5480.0120.561
aggregateSum0.5960.0040.602
aggregateTopn0.5330.0120.547
applyAnovasOnProteins0.1330.0000.133
averageIntensities0.5600.1070.674
barplotEnrichGO_HC 8.660 1.52310.359
barplotGroupGO_HC4.9350.5145.497
boxPlotD_HC0.3590.0400.404
buildGraph1.6810.1441.833
check.conditions0.4280.0080.437
check.design0.4210.0040.426
checkClusterability3.2561.5125.038
classic1wayAnova000
compareNormalizationD_HC0.1780.0200.201
compute.selection.table0.8870.1501.065
compute_t_tests1.5740.2491.874
corrMatrixD_HC0.5950.0400.641
createMSnset1.9330.0752.023
createMSnset21.8370.0741.925
dapar_hc_ExportMenu0.1750.0270.209
dapar_hc_chart0.0810.0040.086
deleteLinesFromIndices0.4950.0200.518
densityPlotD_HC3.5960.9954.752
diffAnaComputeAdjustedPValues0.2550.0200.277
diffAnaComputeFDR000
diffAnaGetSignificant0.3330.0320.375
diffAnaSave0.3000.0360.344
diffAnaVolcanoplot0.1920.0240.219
diffAnaVolcanoplot_rCharts0.4380.0480.490
display.CC.visNet1.7640.1361.906
enrich_GO4.8460.4205.318
finalizeAggregation000
findMECBlock0.5100.0120.525
formatHSDResults000
formatLimmaResult0.2090.0150.229
formatPHResults000
formatPHTResults000
fudge2LRT000
get.pep.prot.cc1.5340.0641.603
getDesignLevel0.4250.0070.433
getIndicesConditions0.4280.0070.437
getIndicesOfLinesToRemove0.4660.0000.468
getListNbValuesInLines0.4310.0120.443
getNumberOf0.4600.0040.466
getNumberOfEmptyLines0.4660.0120.479
getPourcentageOfMV0.4620.0080.473
getProcessingInfo0.4260.0120.439
getProteinsStats0.4930.0120.507
getQuantile4Imp0.1120.0000.113
getTextForAggregation0.0010.0000.000
getTextForAnaDiff0.0010.0000.000
getTextForFiltering000
getTextForGOAnalysis000
getTextForHypothesisTest000
getTextForNewDataset0.0040.0000.003
getTextForNormalization0.0010.0000.000
getTextForpeptideImputation0.0010.0000.000
getTextForproteinImputation0.0010.0000.000
globalAdjPval0.5650.0520.629
group_GO4.7880.3555.198
hc_logFC_DensityPlot0.8360.1821.051
hc_mvTypePlot21.0330.1911.263
heatmapD0.7780.0160.799
heatmapForMissingValues0.2060.0160.225
histPValue_HC0.2550.0430.306
impute.pa20.5170.0240.545
inner.aggregate.iter0.5310.0200.556
inner.aggregate.topn0.5550.0080.566
inner.mean0.4810.0070.491
inner.sum0.4820.0080.493
is.subset0.0000.0000.001
limmaCompleteTest1.9220.0892.027
listSheets000
make.contrast0.4430.0080.451
make.design.10.4430.0070.452
make.design.20.4560.0110.470
make.design.30.5090.0000.511
make.design0.4540.0040.459
match.metacell0.4800.0120.494
metacell.def0.0030.0040.007
metacellHisto_HC0.5370.0070.548
metacellPerLinesHistoPerCondition_HC0.6510.0480.705
metacellPerLinesHisto_HC0.9680.0631.045
metacombine0.2220.0120.239
mvImage2.8760.2283.126
my_hc_ExportMenu0.1900.0310.226
my_hc_chart0.1680.0280.200
nonzero0.0250.0000.025
normalizeMethods.dapar000
pepa.test0.4820.0060.492
pkgs.require000
plotJitter1.6530.1161.776
plotJitter_rCharts1.5160.0311.556
plotPCA_Eigen0.5200.0240.548
plotPCA_Eigen_hc0.4220.0080.433
plotPCA_Ind0.4220.0160.439
plotPCA_Var0.4250.0000.426
postHocTest000
proportionConRev_HC0.0540.0160.072
rbindMSnset0.5170.0350.557
reIntroduceMEC0.4990.0130.514
readExcel000
removeLines0.4700.0150.489
samLRT000
saveParameters0.4250.0050.431
scatterplotEnrichGO_HC4.6740.3295.054
search.metacell.tags0.0060.0040.011
separateAdjPval0.2120.0160.230
splitAdjacencyMat0.4860.0200.508
test.design0.4630.0040.468
testAnovaModels0.1430.0070.152
thresholdpval4fdr000
translatedRandomBeta0.0020.0000.003
univ_AnnotDbPkg0.2040.0310.239
violinPlotD0.3740.0160.392
visualizeClusters1.8870.1602.056
vsn0.7350.0180.755
wrapper.CVDistD_HC2.2870.5032.800
wrapper.compareNormalizationD_HC57.04715.57274.992
wrapper.corrMatrixD_HC0.5860.0200.609
wrapper.dapar.impute.mi19.619 0.75620.558
wrapper.heatmapD0.6450.0120.661
wrapper.impute.KNN0.4790.0070.488
wrapper.impute.detQuant0.5270.0080.536
wrapper.impute.fixedValue0.5200.0190.543
wrapper.impute.mle0.4630.0160.481
wrapper.impute.pa0.1500.0160.169
wrapper.impute.pa20.4710.0190.494
wrapper.impute.slsa0.6620.0360.703
wrapper.mvImage0.2420.0200.263
wrapper.normalizeD0.4450.0000.447
wrapper.pca0.1560.0360.192
wrapperCalibrationPlot0.2280.0080.237
wrapperClassic1wayAnova000
wrapperRunClustering3.0070.2143.231
write.excel0.9310.0761.011
writeMSnsetToCSV0.4470.0200.473
writeMSnsetToExcel1.1700.1031.275