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This page was generated on 2025-08-18 12:03 -0400 (Mon, 18 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4818
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4596
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4538
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4535
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: 2025-08-17 13:45 -0400 (Sun, 17 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 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: 2025-08-17 21:32:42 -0400 (Sun, 17 Aug 2025)
EndedAt: 2025-08-17 21:41:11 -0400 (Sun, 17 Aug 2025)
EllapsedTime: 508.5 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 24.04.3 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 35.606 11.594  47.632
wrapper.dapar.impute.mi          13.499  0.242  13.754
barplotEnrichGO_HC                7.172  0.706   7.894
* 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 
 32.582   1.843  34.446 

Example timings

DAPAR.Rcheck/DAPAR-Ex.timings

nameusersystemelapsed
AggregateMetacell0.5400.0410.581
BuildAdjacencyMatrix0.4520.0210.474
BuildColumnToProteinDataset0.5680.0110.578
BuildMetaCell0.5680.0340.603
CVDistD_HC2.9180.0973.046
Children0.0040.0000.004
CountPep0.4780.0150.495
ExtendPalette0.0230.0010.025
GOAnalysisSave000
GetCC2.5820.0592.641
GetColorsForConditions0.4440.0060.450
GetDetailedNbPeptides0.4690.0230.492
GetDetailedNbPeptidesUsed000
GetIndices_BasedOnConditions0.4500.0120.461
GetIndices_MetacellFiltering0.4570.0090.466
GetIndices_WholeLine0.4520.0100.463
GetIndices_WholeMatrix0.4540.0080.462
GetKeyId0.4280.0180.447
GetMatAdj0.4760.0150.492
GetMetacell000
GetMetacellTags0.4500.0070.457
GetNbPeptidesUsed0.4470.0230.470
GetNbTags000
GetSoftAvailables0.0000.0010.001
GetTypeofData0.4330.0110.444
Get_AllComparisons0.2730.0170.289
GlobalQuantileAlignment0.4590.0140.475
GraphPepProt0.4600.0050.465
LH0000
LH0.lm000
LH10.0010.0000.000
LH1.lm000
LOESS1.1350.0231.157
MeanCentering0.4570.0090.465
MetaCellFiltering0.5920.0100.602
MetacellFilteringScope0.0000.0000.001
Metacell_DIA_NN0.4490.0040.452
Metacell_generic0.3800.0020.382
Metacell_maxquant0.4210.0030.424
Metacell_proline0.3870.0020.389
NumericalFiltering0.4710.0100.481
NumericalgetIndicesOfLinesToRemove0.4410.0070.447
OWAnova0.0070.0000.006
QuantileCentering0.4530.0210.474
SetCC2.4370.1072.545
SetMatAdj0.4820.0110.493
Set_POV_MEC_tags0.4450.0070.452
StringBasedFiltering0.4660.0080.475
StringBasedFiltering20.4700.0070.477
SumByColumns1.2240.0101.234
SymFilteringOperators000
UpdateMetacellAfterImputation0.4510.0100.462
aggregateIter0.5950.0050.600
aggregateIterParallel000
aggregateMean0.5270.0050.533
aggregateSum0.5450.0130.558
aggregateTopn0.5130.0080.520
applyAnovasOnProteins0.1350.0020.136
averageIntensities0.4720.0410.515
barplotEnrichGO_HC7.1720.7067.894
barplotGroupGO_HC4.0850.3454.437
boxPlotD_HC0.2550.0260.280
buildGraph1.7780.0491.827
check.conditions0.4210.0000.422
check.design0.4270.0040.431
checkClusterability2.2400.8313.110
classic1wayAnova000
compareNormalizationD_HC0.1600.0150.176
compute.selection.table0.6630.0680.732
compute_t_tests0.9390.0801.023
corrMatrixD_HC0.5080.0210.529
createMSnset1.5020.0801.583
createMSnset21.4530.0451.499
dapar_hc_ExportMenu0.1070.0240.132
dapar_hc_chart0.0460.0060.052
deleteLinesFromIndices0.4640.0160.480
densityPlotD_HC2.2650.6062.892
diffAnaComputeAdjustedPValues0.1740.0140.187
diffAnaComputeFDR000
diffAnaGetSignificant0.2570.0230.281
diffAnaSave0.2390.0330.273
diffAnaVolcanoplot0.1750.0140.189
diffAnaVolcanoplot_rCharts0.3350.0400.376
display.CC.visNet1.6310.1271.758
enrich_GO3.9670.1894.162
finalizeAggregation000
findMECBlock0.4800.0120.491
formatHSDResults000
formatLimmaResult0.1660.0130.180
formatPHResults000
formatPHTResults000
fudge2LRT000
get.pep.prot.cc1.6130.0371.649
getDesignLevel0.4190.0070.426
getIndicesConditions0.4240.0050.429
getIndicesOfLinesToRemove0.4390.0080.447
getListNbValuesInLines0.4230.0070.431
getNumberOf0.4370.0120.449
getNumberOfEmptyLines0.4530.0080.462
getPourcentageOfMV0.4370.0230.460
getProcessingInfo0.4230.0080.430
getProteinsStats0.4540.0090.463
getQuantile4Imp0.1150.0040.119
getTextForAggregation0.0000.0010.000
getTextForAnaDiff0.0000.0000.001
getTextForFiltering000
getTextForGOAnalysis0.0000.0000.001
getTextForHypothesisTest000
getTextForNewDataset0.0020.0000.001
getTextForNormalization0.0010.0000.000
getTextForpeptideImputation000
getTextForproteinImputation0.0010.0000.000
globalAdjPval0.4140.0210.436
group_GO4.1580.2174.381
hc_logFC_DensityPlot0.5140.1510.668
hc_mvTypePlot21.9840.1662.153
heatmapD0.6800.0220.703
heatmapForMissingValues0.2000.0120.211
histPValue_HC0.2190.0260.245
impute.pa20.4700.0150.487
inner.aggregate.iter0.4770.0180.497
inner.aggregate.topn0.4590.0110.470
inner.mean0.4380.0200.459
inner.sum0.4520.0150.467
is.subset0.0000.0000.001
limmaCompleteTest1.2600.0341.297
listSheets000
make.contrast0.4250.0070.431
make.design.10.4230.0090.432
make.design.20.4280.0060.434
make.design.30.4350.0060.441
make.design0.4270.0060.432
match.metacell0.4410.0080.449
metacell.def0.0030.0020.005
metacellHisto_HC0.4700.0140.485
metacellPerLinesHistoPerCondition_HC0.5730.0360.609
metacellPerLinesHisto_HC0.6500.0660.717
metacombine0.1430.0040.147
mvImage1.8360.0681.907
my_hc_ExportMenu0.1140.0250.139
my_hc_chart0.1090.0220.132
nonzero0.0130.0020.016
normalizeMethods.dapar000
pepa.test0.4460.0090.455
pkgs.require000
plotJitter1.5840.0151.600
plotJitter_rCharts1.5930.0201.613
plotPCA_Eigen0.4970.0170.514
plotPCA_Eigen_hc0.4320.0070.439
plotPCA_Ind0.4300.0110.442
plotPCA_Var0.4230.0110.434
postHocTest000
proportionConRev_HC0.0420.0070.050
rbindMSnset0.5020.0190.521
reIntroduceMEC0.4880.0070.495
readExcel000
removeLines0.4510.0230.475
samLRT000
saveParameters0.4270.0080.435
scatterplotEnrichGO_HC4.1130.1904.310
search.metacell.tags0.0060.0010.007
separateAdjPval0.1970.0080.204
splitAdjacencyMat0.4870.0100.497
test.design0.4550.0070.461
testAnovaModels0.1440.0030.146
thresholdpval4fdr000
translatedRandomBeta0.0000.0010.002
univ_AnnotDbPkg0.1260.0110.137
violinPlotD0.3240.0040.328
visualizeClusters1.0640.0601.126
vsn0.7170.0100.727
wrapper.CVDistD_HC1.6830.4322.129
wrapper.compareNormalizationD_HC35.60611.59447.632
wrapper.corrMatrixD_HC0.5140.0210.537
wrapper.dapar.impute.mi13.499 0.24213.754
wrapper.heatmapD0.6280.0150.644
wrapper.impute.KNN0.4620.0100.471
wrapper.impute.detQuant0.4940.0150.510
wrapper.impute.fixedValue0.5290.0240.554
wrapper.impute.mle0.4650.0180.483
wrapper.impute.pa0.1610.0060.167
wrapper.impute.pa20.4660.0190.485
wrapper.impute.slsa0.5810.0200.601
wrapper.mvImage0.1690.0090.178
wrapper.normalizeD0.4390.0060.444
wrapper.pca0.1690.0110.180
wrapperCalibrationPlot0.2050.0130.219
wrapperClassic1wayAnova000
wrapperRunClustering1.9000.1502.054
write.excel0.8390.0560.897
writeMSnsetToCSV0.4660.0160.481
writeMSnsetToExcel1.0000.0921.096