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This page was generated on 2025-08-04 11:43 -0400 (Mon, 04 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4823
palomino7Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4565
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4603
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4544
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4579
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: 2025-07-31 13:40 -0400 (Thu, 31 Jul 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 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    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 merida1

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: 1.40.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DAPAR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DAPAR_1.40.0.tar.gz
StartedAt: 2025-08-01 02:14:42 -0400 (Fri, 01 Aug 2025)
EndedAt: 2025-08-01 02:34:48 -0400 (Fri, 01 Aug 2025)
EllapsedTime: 1205.3 seconds
RetCode: 0
Status:   OK  
CheckDir: DAPAR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DAPAR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DAPAR_1.40.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/DAPAR.Rcheck’
* using R version 4.5.1 RC (2025-06-05 r88288)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* 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 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 106.254 46.734 174.676
wrapper.dapar.impute.mi           31.272  1.689  39.293
barplotEnrichGO_HC                14.935  2.981  20.480
barplotGroupGO_HC                  9.088  1.358  11.679
checkClusterability                6.256  3.532  10.177
group_GO                           8.769  1.006  11.655
enrich_GO                          8.687  1.020  11.497
scatterplotEnrichGO_HC             8.644  1.001  12.174
densityPlotD_HC                    6.349  2.475  10.092
CVDistD_HC                         7.051  0.236   7.516
wrapper.CVDistD_HC                 4.622  1.753   7.480
mvImage                            5.655  0.311   7.536
wrapperRunClustering               4.547  0.657   6.238
limmaCompleteTest                  4.777  0.151   5.993
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/DAPAR.Rcheck/00check.log’
for details.


Installation output

DAPAR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL DAPAR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/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 version 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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 
 66.027   2.586  77.346 

Example timings

DAPAR.Rcheck/DAPAR-Ex.timings

nameusersystemelapsed
AggregateMetacell1.0940.0421.183
BuildAdjacencyMatrix0.8480.0160.914
BuildColumnToProteinDataset1.0220.0181.123
BuildMetaCell1.0600.0481.160
CVDistD_HC7.0510.2367.516
Children0.0110.0000.012
CountPep0.8730.0150.920
ExtendPalette0.0570.0030.060
GOAnalysisSave0.0000.0010.001
GetCC3.1040.0683.337
GetColorsForConditions0.7960.0140.865
GetDetailedNbPeptides0.8450.0140.939
GetDetailedNbPeptidesUsed0.0000.0000.001
GetIndices_BasedOnConditions0.8250.0140.899
GetIndices_MetacellFiltering0.8480.0170.921
GetIndices_WholeLine0.8390.0180.935
GetIndices_WholeMatrix0.8310.0190.930
GetKeyId0.7900.0170.856
GetMatAdj0.9220.0180.995
GetMetacell0.0000.0010.000
GetMetacellTags0.8190.0190.890
GetNbPeptidesUsed0.8290.0200.900
GetNbTags0.0000.0010.000
GetSoftAvailables0.0010.0010.001
GetTypeofData0.7900.0180.839
Get_AllComparisons0.5160.0280.615
GlobalQuantileAlignment0.8210.0150.873
GraphPepProt0.8360.0170.923
LH0000
LH0.lm0.0000.0000.001
LH10.0000.0000.001
LH1.lm0.0000.0010.000
LOESS1.9990.0302.094
MeanCentering0.8140.0270.852
MetaCellFiltering1.1800.0181.347
MetacellFilteringScope0.0010.0010.001
Metacell_DIA_NN0.8400.0230.944
Metacell_generic0.7810.0260.872
Metacell_maxquant0.8260.0350.887
Metacell_proline0.7790.0240.824
NumericalFiltering0.8950.0190.922
NumericalgetIndicesOfLinesToRemove0.8130.0150.850
OWAnova0.0100.0010.011
QuantileCentering0.8160.0230.867
SetCC2.8950.0313.192
SetMatAdj0.9120.0150.979
Set_POV_MEC_tags0.8280.0190.903
StringBasedFiltering0.8840.0170.947
StringBasedFiltering20.8790.0150.934
SumByColumns3.6710.0353.996
SymFilteringOperators000
UpdateMetacellAfterImputation0.8380.0150.926
aggregateIter1.1870.0171.255
aggregateIterParallel0.0010.0010.001
aggregateMean1.0260.0161.078
aggregateSum1.0830.0171.165
aggregateTopn0.9850.0151.037
applyAnovasOnProteins0.2320.0110.248
averageIntensities1.1800.2251.601
barplotEnrichGO_HC14.935 2.98120.480
barplotGroupGO_HC 9.088 1.35811.679
boxPlotD_HC0.5750.1580.832
buildGraph2.3080.0882.685
check.conditions0.7900.0130.826
check.design0.7830.0140.835
checkClusterability 6.256 3.53210.177
classic1wayAnova0.0000.0010.000
compareNormalizationD_HC0.3040.0960.473
compute.selection.table1.4760.2411.975
compute_t_tests2.4570.3653.360
corrMatrixD_HC1.0150.1501.309
createMSnset3.3240.1643.772
createMSnset23.3180.1813.529
dapar_hc_ExportMenu0.2710.2410.530
dapar_hc_chart0.1130.0820.230
deleteLinesFromIndices0.8960.0391.069
densityPlotD_HC 6.349 2.47510.092
diffAnaComputeAdjustedPValues0.3580.0740.537
diffAnaComputeFDR0.0000.0000.001
diffAnaGetSignificant0.5550.1070.831
diffAnaSave0.5170.0990.754
diffAnaVolcanoplot0.3510.0530.517
diffAnaVolcanoplot_rCharts0.7790.2201.219
display.CC.visNet2.4460.1482.719
enrich_GO 8.687 1.02011.497
finalizeAggregation0.0000.0010.005
findMECBlock0.8830.0291.049
formatHSDResults000
formatLimmaResult0.3290.0510.485
formatPHResults0.0000.0010.001
formatPHTResults0.0000.0010.001
fudge2LRT0.0000.0010.000
get.pep.prot.cc2.1620.1072.511
getDesignLevel0.7960.0150.901
getIndicesConditions0.7890.0150.887
getIndicesOfLinesToRemove0.8370.0280.973
getListNbValuesInLines0.7920.0150.851
getNumberOf0.8390.0290.984
getNumberOfEmptyLines0.8690.0200.931
getPourcentageOfMV0.8400.0260.922
getProcessingInfo0.7980.0140.849
getProteinsStats0.8750.0341.048
getQuantile4Imp0.1880.0100.226
getTextForAggregation0.0010.0010.001
getTextForAnaDiff0.0000.0010.002
getTextForFiltering0.0010.0000.001
getTextForGOAnalysis0.0000.0000.001
getTextForHypothesisTest0.0010.0010.001
getTextForNewDataset0.0030.0010.004
getTextForNormalization0.0010.0000.001
getTextForpeptideImputation0.0000.0000.001
getTextForproteinImputation0.0010.0000.001
globalAdjPval0.9770.0951.324
group_GO 8.769 1.00611.655
hc_logFC_DensityPlot1.3440.5192.138
hc_mvTypePlot21.9020.5312.850
heatmapD1.4090.1121.816
heatmapForMissingValues0.3510.0470.517
histPValue_HC0.4510.1310.648
impute.pa20.9310.0521.160
inner.aggregate.iter0.9470.0481.238
inner.aggregate.topn0.8820.0341.106
inner.mean0.8740.0351.091
inner.sum0.8740.0351.127
is.subset0.0010.0010.003
limmaCompleteTest4.7770.1515.993
listSheets0.0010.0010.001
make.contrast0.7890.0190.982
make.design.10.7900.0190.962
make.design.20.7920.0210.973
make.design.30.7930.0200.983
make.design0.7890.0190.890
match.metacell0.8350.0310.973
metacell.def0.0120.0050.017
metacellHisto_HC0.9500.1361.364
metacellPerLinesHistoPerCondition_HC1.1260.2391.704
metacellPerLinesHisto_HC1.3910.5532.568
metacombine0.4760.0270.604
mvImage5.6550.3117.536
my_hc_ExportMenu0.2730.2450.751
my_hc_chart0.2760.2531.031
nonzero0.0290.0030.039
normalizeMethods.dapar0.0000.0010.001
pepa.test0.8350.0281.023
pkgs.require0.0000.0000.001
plotJitter2.1910.1042.744
plotJitter_rCharts2.2120.1482.824
plotPCA_Eigen0.9740.0731.229
plotPCA_Eigen_hc0.7850.0150.937
plotPCA_Ind0.8000.0180.994
plotPCA_Var0.7910.0140.968
postHocTest0.0000.0010.000
proportionConRev_HC0.1050.0820.330
rbindMSnset1.0030.0701.303
reIntroduceMEC0.9240.0531.275
readExcel0.0000.0010.000
removeLines0.8870.0461.177
samLRT0.0010.0000.001
saveParameters0.7930.0171.018
scatterplotEnrichGO_HC 8.644 1.00112.174
search.metacell.tags0.0180.0050.091
separateAdjPval0.3330.0290.497
splitAdjacencyMat0.8610.0281.058
test.design0.8160.0150.985
testAnovaModels0.2510.0290.403
thresholdpval4fdr0.0000.0000.001
translatedRandomBeta0.0060.0170.024
univ_AnnotDbPkg0.3340.1490.646
violinPlotD0.5930.0470.774
visualizeClusters2.6950.3353.959
vsn1.2910.0391.558
wrapper.CVDistD_HC4.6221.7537.480
wrapper.compareNormalizationD_HC106.254 46.734174.676
wrapper.corrMatrixD_HC1.0080.1411.446
wrapper.dapar.impute.mi31.272 1.68939.293
wrapper.heatmapD1.1700.0781.434
wrapper.impute.KNN0.8810.0411.025
wrapper.impute.detQuant0.9630.0621.212
wrapper.impute.fixedValue1.0110.0851.273
wrapper.impute.mle0.8830.0401.125
wrapper.impute.pa0.2880.0400.401
wrapper.impute.pa20.9070.0511.107
wrapper.impute.slsa1.2140.0841.545
wrapper.mvImage0.3400.0510.523
wrapper.normalizeD0.8070.0170.902
wrapper.pca0.3230.0520.453
wrapperCalibrationPlot0.3840.0590.578
wrapperClassic1wayAnova0.0000.0010.001
wrapperRunClustering4.5470.6576.238
write.excel1.6340.2672.145
writeMSnsetToCSV0.8510.0441.068
writeMSnsetToExcel2.1110.3842.990