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This page was generated on 2025-10-03 12:07 -0400 (Fri, 03 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4845
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4632
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4577
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: 2025-10-02 13:45 -0400 (Thu, 02 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: 2025-10-03 06:18:45 -0000 (Fri, 03 Oct 2025)
EndedAt: 2025-10-03 06:29:47 -0000 (Fri, 03 Oct 2025)
EllapsedTime: 662.5 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 59.401 15.547  78.074
wrapper.dapar.impute.mi          19.863  0.706  20.742
barplotEnrichGO_HC                8.919  1.435  10.539
barplotGroupGO_HC                 5.073  0.526   5.658
enrich_GO                         5.091  0.351   5.499
group_GO                          4.855  0.355   5.258
scatterplotEnrichGO_HC            4.768  0.331   5.153
checkClusterability               3.570  1.194   5.015
* 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 
 42.030   0.902  43.238 

Example timings

DAPAR.Rcheck/DAPAR-Ex.timings

nameusersystemelapsed
AggregateMetacell0.6440.0000.648
BuildAdjacencyMatrix0.4780.0120.491
BuildColumnToProteinDataset0.5710.0160.589
BuildMetaCell0.7470.0360.789
CVDistD_HC4.1890.3064.570
Children0.0060.0000.007
CountPep0.4900.0120.504
ExtendPalette0.0370.0000.037
GOAnalysisSave000
GetCC2.5050.2042.716
GetColorsForConditions0.4440.0030.449
GetDetailedNbPeptides0.4760.0080.486
GetDetailedNbPeptidesUsed000
GetIndices_BasedOnConditions0.4620.0080.471
GetIndices_MetacellFiltering0.4660.0080.475
GetIndices_WholeLine0.4620.0240.487
GetIndices_WholeMatrix0.4690.0040.476
GetKeyId0.4320.0070.441
GetMatAdj0.5180.0200.539
GetMetacell000
GetMetacellTags0.4500.0160.467
GetNbPeptidesUsed0.4540.0120.468
GetNbTags000
GetSoftAvailables0.0010.0000.001
GetTypeofData0.4400.0160.457
Get_AllComparisons0.3180.0280.349
GlobalQuantileAlignment0.4540.0080.468
GraphPepProt0.4580.0240.483
LH0000
LH0.lm000
LH1000
LH1.lm000
LOESS1.8540.0081.868
MeanCentering0.4700.0240.495
MetaCellFiltering0.6690.0240.696
MetacellFilteringScope000
Metacell_DIA_NN0.5460.0040.552
Metacell_generic0.4540.0080.463
Metacell_maxquant0.5070.0080.517
Metacell_proline0.4450.0080.455
NumericalFiltering0.4910.0120.505
NumericalgetIndicesOfLinesToRemove0.4520.0000.455
OWAnova0.0040.0040.008
QuantileCentering0.4750.0230.501
SetCC2.2860.1082.401
SetMatAdj0.4960.0080.505
Set_POV_MEC_tags0.4450.0080.454
StringBasedFiltering0.4910.0040.497
StringBasedFiltering20.5090.0000.514
SumByColumns1.7610.1401.906
SymFilteringOperators000
UpdateMetacellAfterImputation0.4760.0040.481
aggregateIter0.6770.0000.679
aggregateIterParallel000
aggregateMean0.5740.0080.584
aggregateSum0.6090.0000.612
aggregateTopn0.5570.0040.563
applyAnovasOnProteins0.1320.0040.136
averageIntensities0.5750.0710.656
barplotEnrichGO_HC 8.919 1.43510.539
barplotGroupGO_HC5.0730.5265.658
boxPlotD_HC0.3910.0320.430
buildGraph1.7510.2121.969
check.conditions0.4350.0000.436
check.design0.4180.0160.436
checkClusterability3.5701.1945.015
classic1wayAnova000
compareNormalizationD_HC0.1780.0200.200
compute.selection.table0.8930.1241.037
compute_t_tests1.5060.2011.750
corrMatrixD_HC0.6020.0200.627
createMSnset1.8980.0831.998
createMSnset21.8710.0791.965
dapar_hc_ExportMenu0.1730.0430.222
dapar_hc_chart0.0670.0200.087
deleteLinesFromIndices0.5050.0080.516
densityPlotD_HC3.7180.8734.760
diffAnaComputeAdjustedPValues0.2550.0200.276
diffAnaComputeFDR0.0000.0000.001
diffAnaGetSignificant0.3110.0480.363
diffAnaSave0.3180.0200.339
diffAnaVolcanoplot0.1970.0280.226
diffAnaVolcanoplot_rCharts0.4510.0630.521
display.CC.visNet1.7860.2072.008
enrich_GO5.0910.3515.499
finalizeAggregation000
findMECBlock0.4900.0160.509
formatHSDResults000
formatLimmaResult0.1990.0040.204
formatPHResults000
formatPHTResults0.0000.0000.001
fudge2LRT000
get.pep.prot.cc1.6470.0751.727
getDesignLevel0.4230.0040.429
getIndicesConditions0.4280.0040.432
getIndicesOfLinesToRemove0.4650.0000.468
getListNbValuesInLines0.4240.0080.433
getNumberOf0.4490.0160.468
getNumberOfEmptyLines0.4540.0160.471
getPourcentageOfMV0.4630.0030.469
getProcessingInfo0.4200.0040.426
getProteinsStats0.4600.0160.478
getQuantile4Imp0.1110.0000.111
getTextForAggregation0.0010.0000.000
getTextForAnaDiff0.0000.0000.001
getTextForFiltering0.0000.0000.001
getTextForGOAnalysis0.0000.0000.001
getTextForHypothesisTest000
getTextForNewDataset0.0030.0000.003
getTextForNormalization000
getTextForpeptideImputation0.0010.0000.000
getTextForproteinImputation000
globalAdjPval0.5910.0440.644
group_GO4.8550.3555.258
hc_logFC_DensityPlot0.8810.1511.068
hc_mvTypePlot21.0500.1531.235
heatmapD0.7460.0390.792
heatmapForMissingValues0.2180.0120.233
histPValue_HC0.2640.0320.300
impute.pa20.5380.0070.548
inner.aggregate.iter0.5470.0200.570
inner.aggregate.topn0.5540.0200.577
inner.mean0.4950.0040.501
inner.sum0.4960.0000.498
is.subset0.0010.0000.000
limmaCompleteTest1.9660.0712.049
listSheets000
make.contrast0.4620.0040.467
make.design.10.4660.0040.471
make.design.20.4560.0160.473
make.design.30.5170.0120.530
make.design0.4620.0060.470
match.metacell0.5010.0120.516
metacell.def0.0030.0040.007
metacellHisto_HC0.5410.0200.564
metacellPerLinesHistoPerCondition_HC0.6740.0270.708
metacellPerLinesHisto_HC0.9520.0991.065
metacombine0.2500.0350.289
mvImage3.0110.1393.176
my_hc_ExportMenu0.1610.0390.204
my_hc_chart0.1740.0240.204
nonzero0.0260.0000.026
normalizeMethods.dapar000
pepa.test0.4950.0050.501
pkgs.require000
plotJitter1.7460.0791.834
plotJitter_rCharts1.6140.1071.731
plotPCA_Eigen0.5190.0160.541
plotPCA_Eigen_hc0.4230.0040.428
plotPCA_Ind0.4360.0040.441
plotPCA_Var0.4200.0040.426
postHocTest000
proportionConRev_HC0.0530.0150.071
rbindMSnset0.5470.0160.569
reIntroduceMEC0.4900.0280.523
readExcel000
removeLines0.4850.0200.510
samLRT000
saveParameters0.4250.0080.434
scatterplotEnrichGO_HC4.7680.3315.153
search.metacell.tags0.010.000.01
separateAdjPval0.2190.0030.226
splitAdjacencyMat0.4840.0170.502
test.design0.4620.0040.467
testAnovaModels0.1420.0120.155
thresholdpval4fdr000
translatedRandomBeta0.0000.0020.003
univ_AnnotDbPkg0.2400.0130.257
violinPlotD0.3980.0360.439
visualizeClusters1.9650.1932.209
vsn0.7720.0070.789
wrapper.CVDistD_HC2.5200.5643.164
wrapper.compareNormalizationD_HC59.40115.54778.074
wrapper.corrMatrixD_HC0.5900.0280.619
wrapper.dapar.impute.mi19.863 0.70620.742
wrapper.heatmapD0.6450.0260.676
wrapper.impute.KNN0.4690.0320.503
wrapper.impute.detQuant0.5350.0240.561
wrapper.impute.fixedValue0.5450.0230.570
wrapper.impute.mle0.4590.0400.501
wrapper.impute.pa0.1660.0160.182
wrapper.impute.pa20.4770.0320.509
wrapper.impute.slsa0.6880.0510.743
wrapper.mvImage0.2670.0400.308
wrapper.normalizeD0.4580.0040.463
wrapper.pca0.1940.0080.203
wrapperCalibrationPlot0.2110.0400.251
wrapperClassic1wayAnova000
wrapperRunClustering2.9130.3303.256
write.excel1.0050.0901.101
writeMSnsetToCSV0.4550.0230.486
writeMSnsetToExcel1.1440.1761.330