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This page was generated on 2025-09-22 12:06 -0400 (Mon, 22 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: 2025-09-21 13:45 -0400 (Sun, 21 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 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: 2025-09-19 07:39:03 -0000 (Fri, 19 Sep 2025)
EndedAt: 2025-09-19 07:50:03 -0000 (Fri, 19 Sep 2025)
EllapsedTime: 660.5 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 57.142 16.379  76.059
wrapper.dapar.impute.mi          19.678  0.591  20.431
barplotEnrichGO_HC                8.893  1.517  10.619
barplotGroupGO_HC                 4.914  0.593   5.569
enrich_GO                         4.737  0.429   5.217
wrapperRunClustering              4.397  0.714   5.178
group_GO                          4.688  0.409   5.152
checkClusterability               3.420  1.533   5.254
* 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 
 42.730   1.359  44.331 

Example timings

DAPAR.Rcheck/DAPAR-Ex.timings

nameusersystemelapsed
AggregateMetacell0.6500.0160.670
BuildAdjacencyMatrix0.4610.0200.482
BuildColumnToProteinDataset0.5680.0400.610
BuildMetaCell0.7610.0440.811
CVDistD_HC4.1830.4514.709
Children0.0070.0000.007
CountPep0.4940.0240.520
ExtendPalette0.0370.0000.037
GOAnalysisSave000
GetCC2.3980.1912.597
GetColorsForConditions0.4290.0120.442
GetDetailedNbPeptides0.4710.0080.479
GetDetailedNbPeptidesUsed0.0010.0000.000
GetIndices_BasedOnConditions0.4590.0160.476
GetIndices_MetacellFiltering0.4500.0150.467
GetIndices_WholeLine0.4440.0160.462
GetIndices_WholeMatrix0.4410.0080.451
GetKeyId0.4190.0240.445
GetMatAdj0.5050.0160.522
GetMetacell000
GetMetacellTags0.4560.0080.466
GetNbPeptidesUsed0.4660.0000.466
GetNbTags000
GetSoftAvailables0.0000.0000.001
GetTypeofData0.4260.0080.435
Get_AllComparisons0.3280.0280.359
GlobalQuantileAlignment0.4730.0000.480
GraphPepProt0.4660.0110.478
LH0000
LH0.lm000
LH1000
LH1.lm000
LOESS1.8240.0261.854
MeanCentering0.4690.0200.490
MetaCellFiltering0.6840.0160.702
MetacellFilteringScope000
Metacell_DIA_NN0.5200.0280.550
Metacell_generic0.4320.0120.445
Metacell_maxquant0.4950.0120.508
Metacell_proline0.4550.0120.469
NumericalFiltering0.5070.0080.516
NumericalgetIndicesOfLinesToRemove0.4410.0080.450
OWAnova0.0050.0040.009
QuantileCentering0.4810.0000.483
SetCC2.1990.1442.349
SetMatAdj0.4990.0030.504
Set_POV_MEC_tags0.4560.0010.457
StringBasedFiltering0.4850.0030.490
StringBasedFiltering20.4690.0160.487
SumByColumns1.7600.1161.881
SymFilteringOperators0.0000.0000.001
UpdateMetacellAfterImputation0.4590.0060.467
aggregateIter0.6750.0240.702
aggregateIterParallel000
aggregateMean0.5640.0000.566
aggregateSum0.6040.0000.606
aggregateTopn0.5560.0230.581
applyAnovasOnProteins0.1350.0040.139
averageIntensities0.5740.0670.650
barplotEnrichGO_HC 8.893 1.51710.619
barplotGroupGO_HC4.9140.5935.569
boxPlotD_HC0.3100.0430.362
buildGraph1.7170.1511.879
check.conditions0.4290.0150.447
check.design0.4270.0080.436
checkClusterability3.4201.5335.254
classic1wayAnova000
compareNormalizationD_HC0.1830.0160.201
compute.selection.table0.8520.1260.998
compute_t_tests1.4240.1521.610
corrMatrixD_HC0.5680.0350.607
createMSnset1.8210.0641.895
createMSnset21.7820.0551.848
dapar_hc_ExportMenu0.1630.0440.212
dapar_hc_chart0.0730.0150.090
deleteLinesFromIndices0.4680.0360.506
densityPlotD_HC3.4041.0204.584
diffAnaComputeAdjustedPValues0.2470.0280.278
diffAnaComputeFDR000
diffAnaGetSignificant0.3210.0350.363
diffAnaSave0.3080.0360.351
diffAnaVolcanoplot0.1820.0320.217
diffAnaVolcanoplot_rCharts0.4060.0910.507
display.CC.visNet1.6410.2071.860
enrich_GO4.7370.4295.217
finalizeAggregation000
findMECBlock0.4880.0070.499
formatHSDResults000
formatLimmaResult0.1920.0190.218
formatPHResults000
formatPHTResults000
fudge2LRT000
get.pep.prot.cc1.4400.0721.517
getDesignLevel0.4210.0000.421
getIndicesConditions0.4210.0000.423
getIndicesOfLinesToRemove0.4430.0110.457
getListNbValuesInLines0.4180.0080.428
getNumberOf0.4450.0120.459
getNumberOfEmptyLines0.4620.0000.464
getPourcentageOfMV0.4580.0040.463
getProcessingInfo0.4150.0120.429
getProteinsStats0.4630.0040.470
getQuantile4Imp0.1050.0040.109
getTextForAggregation0.0010.0000.000
getTextForAnaDiff000
getTextForFiltering000
getTextForGOAnalysis0.0000.0000.001
getTextForHypothesisTest0.0000.0010.000
getTextForNewDataset0.0020.0010.003
getTextForNormalization000
getTextForpeptideImputation000
getTextForproteinImputation0.0010.0000.000
globalAdjPval0.5800.0240.615
group_GO4.6880.4095.152
hc_logFC_DensityPlot0.8260.1641.022
hc_mvTypePlot21.0350.1241.186
heatmapD0.7330.0230.762
heatmapForMissingValues0.2070.0120.221
histPValue_HC0.2770.0280.309
impute.pa20.5160.0030.522
inner.aggregate.iter0.5060.0390.548
inner.aggregate.topn0.4940.0080.503
inner.mean0.4840.0040.490
inner.sum0.5400.0150.558
is.subset0.0000.0000.001
limmaCompleteTest1.9370.0952.046
listSheets000
make.contrast0.4550.0080.464
make.design.10.4530.0040.459
make.design.20.4590.0080.469
make.design.30.4550.0160.472
make.design0.5110.0160.528
match.metacell0.4780.0080.487
metacell.def0.0070.0000.007
metacellHisto_HC0.5190.0280.549
metacellPerLinesHistoPerCondition_HC0.6490.0430.697
metacellPerLinesHisto_HC0.7870.0710.868
metacombine0.2450.0320.279
mvImage3.0790.1673.278
my_hc_ExportMenu0.1740.0270.206
my_hc_chart0.1430.0510.199
nonzero0.0240.0020.025
normalizeMethods.dapar000
pepa.test0.4960.0040.502
pkgs.require000
plotJitter1.7220.0841.813
plotJitter_rCharts1.6100.0231.643
plotPCA_Eigen0.5270.0080.538
plotPCA_Eigen_hc0.4250.0040.430
plotPCA_Ind0.4340.0040.439
plotPCA_Var0.4270.0000.429
postHocTest000
proportionConRev_HC0.0570.0080.066
rbindMSnset0.5400.0230.569
reIntroduceMEC0.5030.0160.535
readExcel000
removeLines0.4830.0120.498
samLRT000
saveParameters0.4210.0120.435
scatterplotEnrichGO_HC4.6630.2904.985
search.metacell.tags0.0100.0000.011
separateAdjPval0.2220.0070.233
splitAdjacencyMat0.5070.0090.518
test.design0.4760.0000.478
testAnovaModels0.1450.0110.159
thresholdpval4fdr000
translatedRandomBeta0.0000.0030.003
univ_AnnotDbPkg0.2510.0120.267
violinPlotD0.3700.0200.393
visualizeClusters1.8730.2342.132
vsn0.7530.0240.783
wrapper.CVDistD_HC2.5520.6833.417
wrapper.compareNormalizationD_HC57.14216.37976.059
wrapper.corrMatrixD_HC0.5760.0200.598
wrapper.dapar.impute.mi19.678 0.59120.431
wrapper.heatmapD0.6850.0150.703
wrapper.impute.KNN0.4660.0260.496
wrapper.impute.detQuant0.5200.0240.547
wrapper.impute.fixedValue0.5380.0350.578
wrapper.impute.mle0.5360.0120.550
wrapper.impute.pa0.1640.0080.172
wrapper.impute.pa20.4680.0320.506
wrapper.impute.slsa0.6690.0560.727
wrapper.mvImage0.1920.0280.225
wrapper.normalizeD0.5120.0030.517
wrapper.pca0.1880.0080.197
wrapperCalibrationPlot0.2330.0080.243
wrapperClassic1wayAnova000
wrapperRunClustering4.3970.7145.178
write.excel0.9090.1581.090
writeMSnsetToCSV0.4730.0100.490
writeMSnsetToExcel1.2330.1631.423