Back to Multiple platform build/check report for BioC 3.22:   simplified   long
ABC[D]EFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2025-09-20 12:03 -0400 (Sat, 20 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: 2025-09-19 13:45 -0400 (Fri, 19 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 nebbiolo2

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: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:DAPAR.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings DAPAR_1.41.0.tar.gz
StartedAt: 2025-09-19 22:55:09 -0400 (Fri, 19 Sep 2025)
EndedAt: 2025-09-19 23:08:27 -0400 (Fri, 19 Sep 2025)
EllapsedTime: 797.1 seconds
RetCode: 0
Status:   OK  
CheckDir: DAPAR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:DAPAR.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings DAPAR_1.41.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/DAPAR.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* 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 48.609 14.544  76.683
wrapper.dapar.impute.mi          20.430  0.659  26.658
barplotEnrichGO_HC                9.805  0.851  15.024
group_GO                          6.663  0.477   7.417
scatterplotEnrichGO_HC            6.285  0.368   6.746
barplotGroupGO_HC                 6.211  0.265   7.410
* 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/bbs-3.22-bioc/R/bin/R CMD INSTALL DAPAR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/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 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-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 
 46.893   1.488  58.110 

Example timings

DAPAR.Rcheck/DAPAR-Ex.timings

nameusersystemelapsed
AggregateMetacell0.9080.0251.012
BuildAdjacencyMatrix0.7590.0180.778
BuildColumnToProteinDataset0.8820.0310.913
BuildMetaCell0.8120.0180.914
CVDistD_HC4.4870.1214.930
Children0.0070.0000.007
CountPep0.7820.0190.802
ExtendPalette0.0390.0020.040
GOAnalysisSave000
GetCC2.8370.0214.016
GetColorsForConditions0.6050.0151.141
GetDetailedNbPeptides0.6320.0131.312
GetDetailedNbPeptidesUsed000
GetIndices_BasedOnConditions0.6530.0261.316
GetIndices_MetacellFiltering0.6490.0130.766
GetIndices_WholeLine0.7410.0160.757
GetIndices_WholeMatrix0.5860.0150.651
GetKeyId0.6680.0190.762
GetMatAdj0.5700.0200.589
GetMetacell000
GetMetacellTags0.6730.0260.708
GetNbPeptidesUsed0.6660.0230.759
GetNbTags000
GetSoftAvailables0.0000.0000.001
GetTypeofData0.5260.0300.613
Get_AllComparisons0.3240.0070.371
GlobalQuantileAlignment0.7540.0160.834
GraphPepProt0.6450.0080.784
LH0000
LH0.lm000
LH1000
LH1.lm000
LOESS1.5200.0251.548
MeanCentering0.5790.0200.600
MetaCellFiltering0.7260.0190.778
MetacellFilteringScope000
Metacell_DIA_NN0.6470.0060.883
Metacell_generic0.5630.0040.671
Metacell_maxquant0.7410.0040.759
Metacell_proline0.6270.0030.714
NumericalFiltering0.5950.0100.645
NumericalgetIndicesOfLinesToRemove0.5560.0110.587
OWAnova0.0070.0000.008
QuantileCentering0.7100.0180.733
SetCC3.0760.1563.318
SetMatAdj0.7990.0230.829
Set_POV_MEC_tags0.5860.0140.665
StringBasedFiltering0.5900.0220.751
StringBasedFiltering20.5970.0130.665
SumByColumns1.7290.1602.093
SymFilteringOperators0.0010.0000.000
UpdateMetacellAfterImputation0.5680.0090.586
aggregateIter0.7460.0060.753
aggregateIterParallel000
aggregateMean0.6510.0060.657
aggregateSum0.7230.0110.987
aggregateTopn0.6370.0150.666
applyAnovasOnProteins0.1640.0050.168
averageIntensities0.5620.0610.656
barplotEnrichGO_HC 9.805 0.85115.024
barplotGroupGO_HC6.2110.2657.410
boxPlotD_HC0.4320.0430.502
buildGraph2.0780.0942.253
check.conditions0.7140.0160.745
check.design0.7120.0220.741
checkClusterability2.7761.0054.198
classic1wayAnova000
compareNormalizationD_HC0.1930.0140.209
compute.selection.table0.7880.0550.993
compute_t_tests1.3030.0941.535
corrMatrixD_HC0.6920.0580.891
createMSnset2.3180.0772.836
createMSnset22.4290.0522.549
dapar_hc_ExportMenu0.1900.0390.245
dapar_hc_chart0.0870.0110.098
deleteLinesFromIndices0.7530.0200.773
densityPlotD_HC2.5060.4853.032
diffAnaComputeAdjustedPValues0.2090.0130.222
diffAnaComputeFDR000
diffAnaGetSignificant0.2670.0210.290
diffAnaSave0.2480.0180.267
diffAnaVolcanoplot0.1840.0080.193
diffAnaVolcanoplot_rCharts0.3580.0680.425
display.CC.visNet1.9300.1612.091
enrich_GO4.3620.1964.562
finalizeAggregation000
findMECBlock0.6120.0180.645
formatHSDResults000
formatLimmaResult0.2240.0100.233
formatPHResults000
formatPHTResults000
fudge2LRT000
get.pep.prot.cc2.0420.1252.827
getDesignLevel0.7120.0290.818
getIndicesConditions0.5800.0240.658
getIndicesOfLinesToRemove0.5260.0330.559
getListNbValuesInLines0.5330.0060.539
getNumberOf0.5340.0330.606
getNumberOfEmptyLines0.7010.0310.891
getPourcentageOfMV0.7430.0250.768
getProcessingInfo0.6930.0250.719
getProteinsStats0.7480.0330.795
getQuantile4Imp0.1590.0190.177
getTextForAggregation000
getTextForAnaDiff000
getTextForFiltering000
getTextForGOAnalysis0.0010.0000.000
getTextForHypothesisTest000
getTextForNewDataset0.0030.0020.004
getTextForNormalization0.0010.0000.001
getTextForpeptideImputation0.0010.0000.000
getTextForproteinImputation0.0010.0000.000
globalAdjPval0.6690.0770.749
group_GO6.6630.4777.417
hc_logFC_DensityPlot0.9340.2051.140
hc_mvTypePlot21.3720.2291.606
heatmapD0.8720.0590.984
heatmapForMissingValues0.2290.0220.251
histPValue_HC0.2750.0350.336
impute.pa20.6070.0190.663
inner.aggregate.iter0.6280.0250.740
inner.aggregate.topn0.6160.0390.798
inner.mean0.5780.0210.640
inner.sum0.5780.0090.701
is.subset000
limmaCompleteTest2.1350.1372.559
listSheets000
make.contrast0.6350.0200.851
make.design.10.6830.0160.844
make.design.20.6560.0300.763
make.design.30.7670.0250.981
make.design0.5900.0130.974
match.metacell0.6940.0201.004
metacell.def0.0080.0000.008
metacellHisto_HC0.6820.0300.803
metacellPerLinesHistoPerCondition_HC0.7270.0371.240
metacellPerLinesHisto_HC1.0020.0821.478
metacombine0.2200.0340.275
mvImage2.5750.0882.895
my_hc_ExportMenu0.1580.0250.192
my_hc_chart0.1400.0210.183
nonzero0.0170.0000.017
normalizeMethods.dapar000
pepa.test0.5170.0150.550
pkgs.require000
plotJitter2.0790.2692.443
plotJitter_rCharts2.0990.1052.209
plotPCA_Eigen0.8140.0440.858
plotPCA_Eigen_hc0.5740.0110.733
plotPCA_Ind0.6070.0110.682
plotPCA_Var0.7510.0160.811
postHocTest000
proportionConRev_HC0.0560.0160.074
rbindMSnset0.6400.0430.699
reIntroduceMEC0.5800.0270.609
readExcel000
removeLines0.5680.0220.735
samLRT000
saveParameters0.5300.0130.551
scatterplotEnrichGO_HC6.2850.3686.746
search.metacell.tags0.0080.0010.009
separateAdjPval0.2520.0250.276
splitAdjacencyMat0.5910.0170.609
test.design0.7520.0110.767
testAnovaModels0.2020.0060.208
thresholdpval4fdr000
translatedRandomBeta0.0010.0010.003
univ_AnnotDbPkg0.2530.0290.282
violinPlotD0.4930.0170.511
visualizeClusters1.6350.1311.963
vsn1.0140.0081.145
wrapper.CVDistD_HC2.3730.5773.340
wrapper.compareNormalizationD_HC48.60914.54476.683
wrapper.corrMatrixD_HC0.8450.0371.016
wrapper.dapar.impute.mi20.430 0.65926.658
wrapper.heatmapD1.0310.0501.236
wrapper.impute.KNN0.6480.0230.790
wrapper.impute.detQuant0.5920.0340.767
wrapper.impute.fixedValue0.6680.0450.722
wrapper.impute.mle0.7370.0290.959
wrapper.impute.pa0.2290.0240.252
wrapper.impute.pa20.7490.0410.790
wrapper.impute.slsa0.8740.0440.924
wrapper.mvImage0.1990.0230.225
wrapper.normalizeD0.8200.0630.898
wrapper.pca0.2120.0170.294
wrapperCalibrationPlot0.2420.0180.369
wrapperClassic1wayAnova000
wrapperRunClustering2.7650.3753.591
write.excel1.2070.1101.319
writeMSnsetToCSV0.5430.0260.633
writeMSnsetToExcel1.3090.1591.864