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This page was generated on 2025-08-30 12:05 -0400 (Sat, 30 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4615
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4562
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4541
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 512/2320HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DAPAR 1.41.0  (landing page)
Samuel Wieczorek
Snapshot Date: 2025-08-29 13:45 -0400 (Fri, 29 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 24.04.3 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 lconway

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: /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_1.41.0.tar.gz
StartedAt: 2025-08-29 20:14:25 -0400 (Fri, 29 Aug 2025)
EndedAt: 2025-08-29 20:24:57 -0400 (Fri, 29 Aug 2025)
EllapsedTime: 632.1 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_1.41.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/DAPAR.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 ‘1.41.0’
* 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 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 61.684 30.002  91.009
wrapper.dapar.impute.mi          15.393  1.170  16.664
barplotEnrichGO_HC                9.133  1.874  11.070
checkClusterability               4.412  2.865   7.225
barplotGroupGO_HC                 5.624  0.877   6.539
group_GO                          5.315  0.675   6.046
enrich_GO                         5.189  0.653   5.889
scatterplotEnrichGO_HC            5.148  0.656   5.877
densityPlotD_HC                   3.638  1.641   5.269
* 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-3.22-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 ‘1.41.0’
** 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-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 1.41.0.

  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 
 37.307   1.585  44.714 

Example timings

DAPAR.Rcheck/DAPAR-Ex.timings

nameusersystemelapsed
AggregateMetacell0.5280.0260.558
BuildAdjacencyMatrix0.4450.0090.457
BuildColumnToProteinDataset0.5850.0100.600
BuildMetaCell0.7070.0210.734
CVDistD_HC3.1310.1623.327
Children0.0050.0000.005
CountPep0.4770.0050.484
ExtendPalette0.0260.0020.027
GOAnalysisSave000
GetCC2.4870.1292.717
GetColorsForConditions0.4560.0050.464
GetDetailedNbPeptides0.4380.0040.443
GetDetailedNbPeptidesUsed0.0000.0000.001
GetIndices_BasedOnConditions0.4300.0040.434
GetIndices_MetacellFiltering0.4510.0060.459
GetIndices_WholeLine0.4460.0040.452
GetIndices_WholeMatrix0.4370.0050.444
GetKeyId0.4250.0060.433
GetMatAdj0.4880.0090.505
GetMetacell0.0000.0010.000
GetMetacellTags0.4590.0060.466
GetNbPeptidesUsed0.4430.0070.451
GetNbTags0.0000.0000.001
GetSoftAvailables0.0000.0000.001
GetTypeofData0.4350.0070.443
Get_AllComparisons0.2940.0180.314
GlobalQuantileAlignment0.4460.0040.451
GraphPepProt0.4870.0060.494
LH00.0000.0000.001
LH0.lm0.0000.0000.001
LH1000
LH1.lm000
LOESS1.1180.0191.142
MeanCentering0.4720.0160.490
MetaCellFiltering0.5860.0050.594
MetacellFilteringScope0.0000.0010.000
Metacell_DIA_NN0.5570.0120.571
Metacell_generic0.4980.0140.513
Metacell_maxquant0.5430.0200.566
Metacell_proline0.4770.0130.492
NumericalFiltering0.4680.0050.474
NumericalgetIndicesOfLinesToRemove0.4370.0040.443
OWAnova0.0070.0010.007
QuantileCentering0.4420.0090.454
SetCC2.3420.0152.367
SetMatAdj0.4990.0060.508
Set_POV_MEC_tags0.4470.0040.451
StringBasedFiltering0.4880.0040.494
StringBasedFiltering20.4470.0030.451
SumByColumns1.3250.0151.343
SymFilteringOperators000
UpdateMetacellAfterImputation0.4390.0040.447
aggregateIter0.6180.0070.628
aggregateIterParallel000
aggregateMean0.5150.0060.524
aggregateSum0.5660.0060.574
aggregateTopn0.5260.0070.535
applyAnovasOnProteins0.1290.0030.132
averageIntensities0.6420.1400.789
barplotEnrichGO_HC 9.133 1.87411.070
barplotGroupGO_HC5.6240.8776.539
boxPlotD_HC0.2960.1030.399
buildGraph1.8820.0861.978
check.conditions0.4260.0040.432
check.design0.4740.0060.484
checkClusterability4.4122.8657.225
classic1wayAnova000
compareNormalizationD_HC0.1720.0630.237
compute.selection.table0.8980.1961.098
compute_t_tests1.4490.2851.737
corrMatrixD_HC0.6020.0910.695
createMSnset2.2300.1242.378
createMSnset22.1810.1202.330
dapar_hc_ExportMenu0.1550.1730.331
dapar_hc_chart0.0690.0560.126
deleteLinesFromIndices0.5530.0200.575
densityPlotD_HC3.6381.6415.269
diffAnaComputeAdjustedPValues0.2010.0370.238
diffAnaComputeFDR000
diffAnaGetSignificant0.3350.0670.403
diffAnaSave0.3010.0600.361
diffAnaVolcanoplot0.2050.0280.234
diffAnaVolcanoplot_rCharts0.4510.1390.591
display.CC.visNet1.9280.0862.021
enrich_GO5.1890.6535.889
finalizeAggregation000
findMECBlock0.4840.0140.501
formatHSDResults000
formatLimmaResult0.1910.0250.217
formatPHResults000
formatPHTResults000
fudge2LRT000
get.pep.prot.cc1.7290.0781.820
getDesignLevel0.4170.0060.426
getIndicesConditions0.4500.0060.457
getIndicesOfLinesToRemove0.4270.0100.437
getListNbValuesInLines0.4460.0050.453
getNumberOf0.4660.0120.480
getNumberOfEmptyLines0.4790.0090.490
getPourcentageOfMV0.4780.0130.493
getProcessingInfo0.4580.0060.467
getProteinsStats0.4920.0150.509
getQuantile4Imp0.1100.0030.115
getTextForAggregation000
getTextForAnaDiff0.0010.0000.001
getTextForFiltering000
getTextForGOAnalysis000
getTextForHypothesisTest000
getTextForNewDataset0.0020.0010.003
getTextForNormalization000
getTextForpeptideImputation000
getTextForproteinImputation0.0010.0000.001
globalAdjPval0.4800.0550.538
group_GO5.3150.6756.046
hc_logFC_DensityPlot0.7080.3251.031
hc_mvTypePlot22.2650.3382.602
heatmapD0.6740.0570.732
heatmapForMissingValues0.1960.0240.221
histPValue_HC0.2640.0900.357
impute.pa20.5080.0280.551
inner.aggregate.iter0.5530.0280.588
inner.aggregate.topn0.4920.0170.512
inner.mean0.4970.0150.514
inner.sum0.4940.0160.514
is.subset0.0010.0000.001
limmaCompleteTest1.5640.0711.644
listSheets000
make.contrast0.4570.0070.467
make.design.10.4490.0060.458
make.design.20.4220.0060.430
make.design.30.4570.0070.466
make.design0.4840.0080.505
match.metacell0.4960.0150.514
metacell.def0.0050.0030.009
metacellHisto_HC0.5290.0750.615
metacellPerLinesHistoPerCondition_HC0.7070.1410.857
metacellPerLinesHisto_HC0.8300.3371.194
metacombine0.2000.0160.216
mvImage2.4730.1992.690
my_hc_ExportMenu0.1580.1690.331
my_hc_chart0.1550.1670.323
nonzero0.0220.0020.025
normalizeMethods.dapar0.0010.0010.001
pepa.test0.4890.0130.503
pkgs.require000
plotJitter1.7660.0641.839
plotJitter_rCharts1.7310.0971.839
plotPCA_Eigen0.5570.0460.607
plotPCA_Eigen_hc0.4490.0050.456
plotPCA_Ind0.4290.0080.438
plotPCA_Var0.4500.0060.464
postHocTest000
proportionConRev_HC0.0530.0560.112
rbindMSnset0.5510.0390.591
reIntroduceMEC0.5280.0250.555
readExcel0.0000.0010.000
removeLines0.5100.0240.539
samLRT000
saveParameters0.4230.0060.432
scatterplotEnrichGO_HC5.1480.6565.877
search.metacell.tags0.0080.0030.011
separateAdjPval0.1970.0150.213
splitAdjacencyMat0.5300.0160.551
test.design0.4960.0080.509
testAnovaModels0.1550.0130.169
thresholdpval4fdr0.0010.0000.001
translatedRandomBeta0.0020.0110.013
univ_AnnotDbPkg0.2450.0890.338
violinPlotD0.3910.0310.428
visualizeClusters1.3560.2241.589
vsn0.8180.0250.855
wrapper.CVDistD_HC2.5081.1543.657
wrapper.compareNormalizationD_HC61.68430.00291.009
wrapper.corrMatrixD_HC0.5950.0820.679
wrapper.dapar.impute.mi15.393 1.17016.664
wrapper.heatmapD0.6890.0380.730
wrapper.impute.KNN0.5340.0200.554
wrapper.impute.detQuant0.6240.0390.671
wrapper.impute.fixedValue0.6000.0410.645
wrapper.impute.mle0.5190.0220.546
wrapper.impute.pa0.1580.0190.178
wrapper.impute.pa20.5260.0280.561
wrapper.impute.slsa0.7210.0620.789
wrapper.mvImage0.1880.0260.214
wrapper.normalizeD0.4860.0080.498
wrapper.pca0.1780.0230.200
wrapperCalibrationPlot0.2270.0320.260
wrapperClassic1wayAnova0.0010.0000.001
wrapperRunClustering2.4470.4422.893
write.excel0.9110.1651.084
writeMSnsetToCSV0.4550.0200.492
writeMSnsetToExcel1.1720.2571.446