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This page was generated on 2025-08-08 12:05 -0400 (Fri, 08 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4815
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4550
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4592
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4534
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 511/2315HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DAPAR 1.41.0  (landing page)
Samuel Wieczorek
Snapshot Date: 2025-08-07 13:45 -0400 (Thu, 07 Aug 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 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    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 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


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: 2025-08-07 21:36:40 -0400 (Thu, 07 Aug 2025)
EndedAt: 2025-08-07 21:45:09 -0400 (Thu, 07 Aug 2025)
EllapsedTime: 509.4 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 (2025-06-13)
* 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 24.04.2 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 35.628 11.753  47.792
wrapper.dapar.impute.mi          14.733  0.489  15.236
barplotEnrichGO_HC                7.223  0.739   7.990
* 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 (2025-06-13) -- "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 
 33.748   2.313  36.166 

Example timings

DAPAR.Rcheck/DAPAR-Ex.timings

nameusersystemelapsed
AggregateMetacell0.5470.0300.578
BuildAdjacencyMatrix0.4550.0190.474
BuildColumnToProteinDataset0.5540.0100.564
BuildMetaCell0.5820.0180.601
CVDistD_HC2.9310.0743.025
Children0.0040.0010.004
CountPep0.4800.0130.494
ExtendPalette0.0240.0020.025
GOAnalysisSave000
GetCC2.5370.1102.649
GetColorsForConditions0.4470.0090.456
GetDetailedNbPeptides0.4720.0100.481
GetDetailedNbPeptidesUsed000
GetIndices_BasedOnConditions0.4460.0100.456
GetIndices_MetacellFiltering0.4590.0070.467
GetIndices_WholeLine0.4510.0070.459
GetIndices_WholeMatrix0.4540.0100.464
GetKeyId0.4580.0160.474
GetMatAdj0.4970.0160.513
GetMetacell000
GetMetacellTags0.4540.0100.464
GetNbPeptidesUsed0.4500.0140.464
GetNbTags0.0000.0000.001
GetSoftAvailables000
GetTypeofData0.4420.0100.453
Get_AllComparisons0.2780.0140.291
GlobalQuantileAlignment0.4680.0110.481
GraphPepProt0.4560.0050.460
LH0000
LH0.lm000
LH1000
LH1.lm000
LOESS1.1520.0341.186
MeanCentering0.4650.0190.484
MetaCellFiltering0.5890.0290.619
MetacellFilteringScope0.0000.0000.001
Metacell_DIA_NN0.5180.0100.527
Metacell_generic0.3980.0040.401
Metacell_maxquant0.4030.0020.405
Metacell_proline0.3680.0030.372
NumericalFiltering0.4730.0080.480
NumericalgetIndicesOfLinesToRemove0.4330.0100.443
OWAnova0.0050.0010.006
QuantileCentering0.4480.0110.458
SetCC2.1690.0552.224
SetMatAdj0.4660.0070.473
Set_POV_MEC_tags0.4340.0100.443
StringBasedFiltering0.4670.0060.473
StringBasedFiltering20.4680.0060.473
SumByColumns1.2210.0081.229
SymFilteringOperators000
UpdateMetacellAfterImputation0.4830.0130.496
aggregateIter0.5770.0090.586
aggregateIterParallel000
aggregateMean0.5040.0170.521
aggregateSum0.5400.0130.553
aggregateTopn0.5030.0110.514
applyAnovasOnProteins0.1310.0060.136
averageIntensities0.4470.0490.499
barplotEnrichGO_HC7.2230.7397.990
barplotGroupGO_HC4.2730.3344.616
boxPlotD_HC0.2550.0260.282
buildGraph1.8140.1011.916
check.conditions0.4310.0010.432
check.design0.4480.0010.448
checkClusterability2.3620.8223.224
classic1wayAnova000
compareNormalizationD_HC0.1660.0100.176
compute.selection.table0.6600.0370.698
compute_t_tests1.0120.0631.078
corrMatrixD_HC0.5150.0410.556
createMSnset1.6110.0761.688
createMSnset21.5710.0371.608
dapar_hc_ExportMenu0.1140.0220.137
dapar_hc_chart0.0510.0100.061
deleteLinesFromIndices0.4850.0180.503
densityPlotD_HC2.4630.7483.223
diffAnaComputeAdjustedPValues0.1870.0080.196
diffAnaComputeFDR000
diffAnaGetSignificant0.2690.0230.293
diffAnaSave0.2500.0230.275
diffAnaVolcanoplot0.1930.0090.202
diffAnaVolcanoplot_rCharts0.3550.0500.406
display.CC.visNet1.8780.0481.927
enrich_GO4.0430.2724.321
finalizeAggregation0.0000.0000.001
findMECBlock0.470.010.48
formatHSDResults000
formatLimmaResult0.1730.0100.184
formatPHResults000
formatPHTResults000
fudge2LRT000
get.pep.prot.cc1.7790.0121.791
getDesignLevel0.4260.0080.435
getIndicesConditions0.4230.0090.433
getIndicesOfLinesToRemove0.4440.0120.456
getListNbValuesInLines0.4360.0070.442
getNumberOf0.4500.0120.461
getNumberOfEmptyLines0.4670.0090.476
getPourcentageOfMV0.4450.0150.460
getProcessingInfo0.4210.0090.429
getProteinsStats0.4530.0100.463
getQuantile4Imp0.1150.0040.119
getTextForAggregation0.0010.0000.001
getTextForAnaDiff000
getTextForFiltering000
getTextForGOAnalysis0.0010.0000.001
getTextForHypothesisTest000
getTextForNewDataset0.0020.0000.002
getTextForNormalization000
getTextForpeptideImputation0.0010.0000.001
getTextForproteinImputation000
globalAdjPval0.4070.0150.423
group_GO4.1360.1934.338
hc_logFC_DensityPlot0.5150.1240.642
hc_mvTypePlot21.9370.1132.053
heatmapD0.7440.0130.756
heatmapForMissingValues0.2010.0050.206
histPValue_HC0.2180.0200.238
impute.pa20.4640.0160.481
inner.aggregate.iter0.4710.0120.483
inner.aggregate.topn0.4550.0040.459
inner.mean0.4470.0050.452
inner.sum0.4450.0020.448
is.subset0.0010.0000.001
limmaCompleteTest1.4020.0291.431
listSheets000
make.contrast0.4270.0010.428
make.design.10.4310.0000.430
make.design.20.4280.0000.428
make.design.30.4290.0010.431
make.design0.4320.0000.432
match.metacell0.4480.0040.452
metacell.def0.0040.0000.004
metacellHisto_HC0.4780.0080.486
metacellPerLinesHistoPerCondition_HC0.5770.0200.597
metacellPerLinesHisto_HC0.6590.0580.718
metacombine0.1450.0050.151
mvImage1.9180.0561.976
my_hc_ExportMenu0.1060.0270.133
my_hc_chart0.1140.0220.136
nonzero0.0160.0000.016
normalizeMethods.dapar000
pepa.test0.4480.0000.448
pkgs.require000
plotJitter1.6330.0821.715
plotJitter_rCharts1.6560.0141.672
plotPCA_Eigen0.4970.0080.505
plotPCA_Eigen_hc0.4270.0010.427
plotPCA_Ind0.4240.0110.435
plotPCA_Var0.4170.0040.422
postHocTest000
proportionConRev_HC0.0400.0090.049
rbindMSnset0.4960.0110.508
reIntroduceMEC0.4710.0050.477
readExcel000
removeLines0.4560.0060.462
samLRT000
saveParameters0.4210.0020.423
scatterplotEnrichGO_HC3.8860.1984.090
search.metacell.tags0.0060.0000.006
separateAdjPval0.1990.0030.202
splitAdjacencyMat0.4750.0100.485
test.design0.4570.0130.470
testAnovaModels0.1410.0110.152
thresholdpval4fdr000
translatedRandomBeta0.0010.0010.002
univ_AnnotDbPkg0.1520.0170.168
violinPlotD0.3230.0130.336
visualizeClusters1.0790.0971.180
vsn0.7060.0080.713
wrapper.CVDistD_HC1.6970.5262.234
wrapper.compareNormalizationD_HC35.62811.75347.792
wrapper.corrMatrixD_HC0.5110.0260.537
wrapper.dapar.impute.mi14.733 0.48915.236
wrapper.heatmapD0.6840.0190.704
wrapper.impute.KNN0.4700.0060.476
wrapper.impute.detQuant0.4960.0130.510
wrapper.impute.fixedValue0.4900.0230.514
wrapper.impute.mle0.4900.0110.501
wrapper.impute.pa0.1540.0040.159
wrapper.impute.pa20.4680.0070.476
wrapper.impute.slsa0.5720.0270.600
wrapper.mvImage0.1740.0100.185
wrapper.normalizeD0.4350.0100.445
wrapper.pca0.1660.0080.174
wrapperCalibrationPlot0.1920.0170.210
wrapperClassic1wayAnova000
wrapperRunClustering1.9010.1682.076
write.excel0.7490.0680.818
writeMSnsetToCSV0.4800.0090.488
writeMSnsetToExcel0.9240.1001.027