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This page was generated on 2025-08-09 12:06 -0400 (Sat, 09 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4818
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4553
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4595
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4537
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 511/2317HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DAPAR 1.41.0  (landing page)
Samuel Wieczorek
Snapshot Date: 2025-08-08 13:45 -0400 (Fri, 08 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 palomino8

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: F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:DAPAR.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings DAPAR_1.41.0.tar.gz
StartedAt: 2025-08-09 01:08:32 -0400 (Sat, 09 Aug 2025)
EndedAt: 2025-08-09 01:19:25 -0400 (Sat, 09 Aug 2025)
EllapsedTime: 652.6 seconds
RetCode: 0
Status:   OK  
CheckDir: DAPAR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:DAPAR.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings DAPAR_1.41.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.22-bioc/meat/DAPAR.Rcheck'
* using R version 4.5.1 (2025-06-13 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* 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 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 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 35.00   1.07   36.28
wrapper.dapar.impute.mi          30.65   0.50   33.05
barplotEnrichGO_HC                8.30   0.81    9.55
barplotGroupGO_HC                 5.26   0.22    5.48
scatterplotEnrichGO_HC            4.87   0.32    5.17
group_GO                          4.83   0.25    5.07
CVDistD_HC                        3.60   0.23   12.91
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  'F:/biocbuild/bbs-3.22-bioc/meat/DAPAR.Rcheck/00check.log'
for details.


Installation output

DAPAR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD INSTALL DAPAR
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.22-bioc/R/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 ucrt) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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 
  55.31    2.00   57.48 

Example timings

DAPAR.Rcheck/DAPAR-Ex.timings

nameusersystemelapsed
AggregateMetacell0.620.040.67
BuildAdjacencyMatrix0.550.020.56
BuildColumnToProteinDataset0.610.000.63
BuildMetaCell0.790.030.87
CVDistD_HC 3.60 0.2312.91
Children0.010.000.02
CountPep0.420.020.43
ExtendPalette0.040.010.05
GOAnalysisSave000
GetCC2.930.002.94
GetColorsForConditions0.490.040.51
GetDetailedNbPeptides0.530.000.54
GetDetailedNbPeptidesUsed000
GetIndices_BasedOnConditions0.510.000.51
GetIndices_MetacellFiltering0.410.030.43
GetIndices_WholeLine0.420.030.46
GetIndices_WholeMatrix0.470.030.50
GetKeyId0.280.060.34
GetMatAdj0.590.030.63
GetMetacell000
GetMetacellTags0.350.050.39
GetNbPeptidesUsed0.500.020.52
GetNbTags000
GetSoftAvailables000
GetTypeofData0.320.010.34
Get_AllComparisons0.300.020.35
GlobalQuantileAlignment0.410.000.43
GraphPepProt0.430.030.47
LH0000
LH0.lm000
LH1000
LH1.lm000
LOESS0.940.030.97
MeanCentering0.380.000.38
MetaCellFiltering0.480.000.48
MetacellFilteringScope000
Metacell_DIA_NN0.520.010.53
Metacell_generic0.450.020.47
Metacell_maxquant0.530.000.53
Metacell_proline0.630.020.64
NumericalFiltering0.340.030.38
NumericalgetIndicesOfLinesToRemove0.410.010.42
OWAnova0.010.000.01
QuantileCentering0.520.000.52
SetCC2.500.072.56
SetMatAdj0.470.000.47
Set_POV_MEC_tags0.380.030.40
StringBasedFiltering0.540.010.57
StringBasedFiltering20.470.020.48
SumByColumns1.390.041.44
SymFilteringOperators000
UpdateMetacellAfterImputation0.500.000.53
aggregateIter0.570.040.59
aggregateIterParallel000
aggregateMean0.500.060.56
aggregateSum0.600.030.63
aggregateTopn0.570.050.62
applyAnovasOnProteins0.160.000.16
averageIntensities0.640.120.92
barplotEnrichGO_HC8.300.819.55
barplotGroupGO_HC5.260.225.48
boxPlotD_HC0.360.050.41
buildGraph1.880.021.89
check.conditions0.290.010.31
check.design0.290.050.33
checkClusterability1.920.082.12
classic1wayAnova000
compareNormalizationD_HC0.200.070.28
compute.selection.table0.640.142.71
compute_t_tests1.130.131.25
corrMatrixD_HC0.560.080.64
createMSnset2.640.062.70
createMSnset22.620.082.70
dapar_hc_ExportMenu0.110.200.36
dapar_hc_chart0.080.030.19
deleteLinesFromIndices0.550.020.56
densityPlotD_HC2.110.252.38
diffAnaComputeAdjustedPValues0.170.010.19
diffAnaComputeFDR000
diffAnaGetSignificant0.250.000.25
diffAnaSave0.280.000.28
diffAnaVolcanoplot0.200.020.22
diffAnaVolcanoplot_rCharts0.350.050.42
display.CC.visNet1.900.034.48
enrich_GO4.630.314.95
finalizeAggregation000
findMECBlock0.530.020.55
formatHSDResults000
formatLimmaResult0.170.010.19
formatPHResults000
formatPHTResults000
fudge2LRT000
get.pep.prot.cc1.750.051.80
getDesignLevel0.530.010.54
getIndicesConditions0.410.040.44
getIndicesOfLinesToRemove0.480.000.48
getListNbValuesInLines0.440.010.46
getNumberOf0.420.030.45
getNumberOfEmptyLines0.460.000.45
getPourcentageOfMV0.50.00.5
getProcessingInfo0.370.000.38
getProteinsStats0.550.020.56
getQuantile4Imp0.140.000.14
getTextForAggregation000
getTextForAnaDiff000
getTextForFiltering000
getTextForGOAnalysis000
getTextForHypothesisTest000
getTextForNewDataset000
getTextForNormalization000
getTextForpeptideImputation000
getTextForproteinImputation0.010.000.02
globalAdjPval0.550.010.58
group_GO4.830.255.07
hc_logFC_DensityPlot0.530.030.58
hc_mvTypePlot22.270.052.33
heatmapD0.810.030.93
heatmapForMissingValues0.220.000.22
histPValue_HC0.200.080.30
impute.pa20.530.000.53
inner.aggregate.iter0.550.000.55
inner.aggregate.topn0.390.010.40
inner.mean0.350.020.37
inner.sum0.570.000.57
is.subset000
limmaCompleteTest1.540.031.57
listSheets000
make.contrast0.490.010.50
make.design.10.470.040.50
make.design.20.470.010.49
make.design.30.430.000.44
make.design0.530.000.53
match.metacell0.500.020.51
metacell.def000
metacellHisto_HC0.540.090.63
metacellPerLinesHistoPerCondition_HC0.680.140.87
metacellPerLinesHisto_HC0.750.311.58
metacombine0.180.000.17
mvImage2.280.142.43
my_hc_ExportMenu0.180.160.37
my_hc_chart0.140.160.31
nonzero0.020.000.01
normalizeMethods.dapar000
pepa.test0.460.010.49
pkgs.require0.000.000.19
plotJitter1.880.021.89
plotJitter_rCharts1.820.051.91
plotPCA_Eigen0.500.040.55
plotPCA_Eigen_hc0.470.020.48
plotPCA_Ind0.380.010.70
plotPCA_Var0.430.000.44
postHocTest000
proportionConRev_HC0.100.050.14
rbindMSnset0.480.000.49
reIntroduceMEC0.550.020.56
readExcel000
removeLines0.470.030.50
samLRT000
saveParameters0.430.010.44
scatterplotEnrichGO_HC4.870.325.17
search.metacell.tags0.020.000.02
separateAdjPval0.250.000.25
splitAdjacencyMat0.530.000.53
test.design0.480.000.48
testAnovaModels0.140.000.14
thresholdpval4fdr000
translatedRandomBeta0.000.010.02
univ_AnnotDbPkg0.270.030.30
violinPlotD0.450.051.47
visualizeClusters1.250.051.29
vsn0.750.030.78
wrapper.CVDistD_HC1.330.111.47
wrapper.compareNormalizationD_HC35.00 1.0736.28
wrapper.corrMatrixD_HC0.550.110.66
wrapper.dapar.impute.mi30.65 0.5033.05
wrapper.heatmapD0.690.070.75
wrapper.impute.KNN0.470.040.51
wrapper.impute.detQuant0.510.000.52
wrapper.impute.fixedValue0.580.000.58
wrapper.impute.mle0.520.020.53
wrapper.impute.pa0.140.010.17
wrapper.impute.pa20.560.040.59
wrapper.impute.slsa0.660.010.68
wrapper.mvImage0.190.000.18
wrapper.normalizeD0.460.060.53
wrapper.pca0.190.000.19
wrapperCalibrationPlot0.190.020.20
wrapperClassic1wayAnova000
wrapperRunClustering2.450.112.72
write.excel0.920.082.91
writeMSnsetToCSV0.520.010.73
writeMSnsetToExcel0.950.081.25