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This page was generated on 2025-10-09 11:41 -0400 (Thu, 09 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4832
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4613
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4554
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4585
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 515/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DAPAR 1.40.0  (landing page)
Samuel Wieczorek
Snapshot Date: 2025-10-06 13:40 -0400 (Mon, 06 Oct 2025)
git_url: https://git.bioconductor.org/packages/DAPAR
git_branch: RELEASE_3_21
git_last_commit: e38913f
git_last_commit_date: 2025-04-15 10:53:48 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for DAPAR on kunpeng2

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: 1.40.0
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_1.40.0.tar.gz
StartedAt: 2025-10-07 08:22:31 -0000 (Tue, 07 Oct 2025)
EndedAt: 2025-10-07 08:33:26 -0000 (Tue, 07 Oct 2025)
EllapsedTime: 655.3 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_1.40.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/DAPAR.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* 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-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DAPAR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DAPAR’ version ‘1.40.0’
* 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 55.772 17.805  76.489
wrapper.dapar.impute.mi          20.181  0.663  21.016
barplotEnrichGO_HC                9.246  1.020  10.425
barplotGroupGO_HC                 5.105  0.469   5.633
scatterplotEnrichGO_HC            5.168  0.365   5.578
enrich_GO                         5.110  0.274   5.428
group_GO                          5.138  0.191   5.373
* 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-3.21-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-devel_2025-02-19/site-library’
* installing *source* package ‘DAPAR’ ...
** this is package ‘DAPAR’ version ‘1.40.0’
** 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 Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
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 1.40.0.

  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 
 42.027   1.179  43.408 

Example timings

DAPAR.Rcheck/DAPAR-Ex.timings

nameusersystemelapsed
AggregateMetacell0.4310.0170.453
BuildAdjacencyMatrix0.3720.0070.381
BuildColumnToProteinDataset0.4130.0040.418
BuildMetaCell1.7090.1471.863
CVDistD_HC3.1480.1443.347
Children0.0070.0000.007
CountPep0.3170.0080.326
ExtendPalette0.0340.0040.039
GOAnalysisSave000
GetCC2.6890.2122.907
GetColorsForConditions0.2620.0000.264
GetDetailedNbPeptides0.2920.0000.293
GetDetailedNbPeptidesUsed000
GetIndices_BasedOnConditions0.2830.0120.295
GetIndices_MetacellFiltering0.2920.0000.292
GetIndices_WholeLine0.2800.0040.284
GetIndices_WholeMatrix0.2860.0000.286
GetKeyId0.2590.0110.272
GetMatAdj0.3410.0120.354
GetMetacell000
GetMetacellTags0.2740.0120.286
GetNbPeptidesUsed0.2790.0120.291
GetNbTags000
GetSoftAvailables0.0010.0000.001
GetTypeofData0.2540.0120.266
Get_AllComparisons0.2780.0400.325
GlobalQuantileAlignment0.2910.0030.298
GraphPepProt0.2950.0080.304
LH0000
LH0.lm000
LH1000
LH1.lm000
LOESS1.6830.0121.698
MeanCentering0.2830.0310.315
MetaCellFiltering0.5000.0080.509
MetacellFilteringScope000
Metacell_DIA_NN0.5340.0080.543
Metacell_generic0.4610.0120.475
Metacell_maxquant0.5200.0040.526
Metacell_proline0.4460.0200.467
NumericalFiltering0.3220.0120.334
NumericalgetIndicesOfLinesToRemove0.2810.0000.282
OWAnova0.0080.0000.008
QuantileCentering0.3350.0160.352
SetCC2.4750.1122.592
SetMatAdj0.3390.0000.340
Set_POV_MEC_tags0.2840.0000.285
StringBasedFiltering0.3210.0000.322
StringBasedFiltering20.3140.0000.314
SumByColumns1.6850.0001.690
SymFilteringOperators000
UpdateMetacellAfterImputation0.2990.0040.304
aggregateIter0.4900.0150.507
aggregateIterParallel000
aggregateMean0.4030.0010.404
aggregateSum0.4320.0040.437
aggregateTopn0.3810.0070.389
applyAnovasOnProteins0.0950.0000.096
averageIntensities0.5640.0560.628
barplotEnrichGO_HC 9.246 1.02010.425
barplotGroupGO_HC5.1050.4695.633
boxPlotD_HC0.3090.0330.348
buildGraph1.7850.0671.859
check.conditions0.2550.0000.255
check.design0.2520.0040.258
checkClusterability3.0401.1964.461
classic1wayAnova000
compareNormalizationD_HC0.1280.0160.146
compute.selection.table0.8260.0790.926
compute_t_tests1.2430.1591.434
corrMatrixD_HC0.4180.0280.450
createMSnset1.9010.0881.996
createMSnset21.9060.0711.987
dapar_hc_ExportMenu0.1680.0400.213
dapar_hc_chart0.0800.0080.088
deleteLinesFromIndices0.3370.0080.347
densityPlotD_HC3.3270.8964.384
diffAnaComputeAdjustedPValues0.1540.0160.171
diffAnaComputeFDR000
diffAnaGetSignificant0.2740.0240.302
diffAnaSave0.2540.0230.283
diffAnaVolcanoplot0.1520.0160.170
diffAnaVolcanoplot_rCharts0.3760.0560.439
display.CC.visNet1.8600.0881.958
enrich_GO5.1100.2745.428
finalizeAggregation000
findMECBlock0.3220.0120.335
formatHSDResults000
formatLimmaResult0.1410.0160.160
formatPHResults000
formatPHTResults000
fudge2LRT000
get.pep.prot.cc1.6860.0831.774
getDesignLevel0.2620.0000.263
getIndicesConditions0.2600.0030.264
getIndicesOfLinesToRemove0.2780.0080.287
getListNbValuesInLines0.2590.0000.260
getNumberOf0.2840.0040.289
getNumberOfEmptyLines0.2960.0080.305
getPourcentageOfMV0.2840.0080.294
getProcessingInfo0.2600.0040.264
getProteinsStats0.2980.0080.308
getQuantile4Imp0.0590.0040.063
getTextForAggregation000
getTextForAnaDiff000
getTextForFiltering000
getTextForGOAnalysis0.0010.0000.001
getTextForHypothesisTest000
getTextForNewDataset0.0020.0000.002
getTextForNormalization000
getTextForpeptideImputation000
getTextForproteinImputation0.0010.0000.001
globalAdjPval0.5030.0350.548
group_GO5.1380.1915.373
hc_logFC_DensityPlot0.6850.1820.894
hc_mvTypePlot20.8120.1851.024
heatmapD0.6800.0270.712
heatmapForMissingValues0.1660.0120.180
histPValue_HC0.2190.0310.256
impute.pa20.3280.0240.354
inner.aggregate.iter0.3610.0000.363
inner.aggregate.topn0.3160.0040.321
inner.mean0.3120.0000.313
inner.sum0.3090.0080.319
is.subset0.0000.0000.001
limmaCompleteTest1.8210.0561.893
listSheets000
make.contrast0.3360.0040.341
make.design.10.2890.0000.289
make.design.20.2890.0040.294
make.design.30.2950.0000.296
make.design0.2920.0040.296
match.metacell0.3260.0040.331
metacell.def0.0070.0000.008
metacellHisto_HC0.3560.0160.375
metacellPerLinesHistoPerCondition_HC1.8280.1031.940
metacellPerLinesHisto_HC0.6160.0670.692
metacombine0.2630.0080.274
mvImage2.7440.1242.903
my_hc_ExportMenu0.1510.0430.198
my_hc_chart0.1640.0330.200
nonzero0.0230.0000.024
normalizeMethods.dapar000
pepa.test0.2810.0090.291
pkgs.require000
plotJitter1.6960.0401.741
plotJitter_rCharts1.6630.0321.701
plotPCA_Eigen0.3610.0160.380
plotPCA_Eigen_hc0.2630.0000.264
plotPCA_Ind0.2670.0040.272
plotPCA_Var0.2620.0000.263
postHocTest000
proportionConRev_HC0.0560.0160.072
rbindMSnset0.3840.0270.416
reIntroduceMEC0.3450.0160.364
readExcel000
removeLines0.3120.0120.326
samLRT000
saveParameters0.2670.0000.267
scatterplotEnrichGO_HC5.1680.3655.578
search.metacell.tags0.0100.0000.011
separateAdjPval0.1750.0040.180
splitAdjacencyMat0.3230.0040.329
test.design0.2920.0080.301
testAnovaModels0.1010.0040.106
thresholdpval4fdr0.0000.0000.001
translatedRandomBeta0.0020.0000.003
univ_AnnotDbPkg0.2180.0200.241
violinPlotD0.3330.0080.344
visualizeClusters1.4540.1561.644
vsn0.6980.0080.709
wrapper.CVDistD_HC2.3350.6083.057
wrapper.compareNormalizationD_HC55.77217.80576.489
wrapper.corrMatrixD_HC0.4140.0320.451
wrapper.dapar.impute.mi20.181 0.66321.016
wrapper.heatmapD0.4740.0110.487
wrapper.impute.KNN0.3440.0080.354
wrapper.impute.detQuant0.3600.0160.378
wrapper.impute.fixedValue0.3560.0120.371
wrapper.impute.mle0.3080.0040.313
wrapper.impute.pa0.1100.0110.122
wrapper.impute.pa20.3050.0160.322
wrapper.impute.slsa0.5000.0520.559
wrapper.mvImage0.1560.0240.183
wrapper.normalizeD0.2900.0080.299
wrapper.pca0.1450.0120.157
wrapperCalibrationPlot0.1920.0120.205
wrapperClassic1wayAnova000
wrapperRunClustering2.8490.4513.376
write.excel0.7470.0750.834
writeMSnsetToCSV0.2920.0040.301
writeMSnsetToExcel0.9610.1571.142