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This page was generated on 2025-09-29 11:38 -0400 (Mon, 29 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4827
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4608
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4549
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4580
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: 2025-09-25 13:40 -0400 (Thu, 25 Sep 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 24.04.3 LTS) / x86_64  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: 2025-09-26 02:27:12 -0400 (Fri, 26 Sep 2025)
EndedAt: 2025-09-26 02:47:30 -0400 (Fri, 26 Sep 2025)
EllapsedTime: 1218.1 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_1.40.0.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 107.085 46.271 176.049
wrapper.dapar.impute.mi           30.725  1.715  39.687
barplotEnrichGO_HC                15.121  3.021  19.940
barplotGroupGO_HC                  8.911  1.220  10.758
group_GO                           8.813  1.034  11.319
enrich_GO                          8.818  1.027  11.332
checkClusterability                6.249  3.579  10.287
scatterplotEnrichGO_HC             8.687  0.997  11.942
densityPlotD_HC                    6.395  2.515   9.501
wrapperRunClustering               6.208  0.747   7.955
CVDistD_HC                         6.213  0.289   7.006
wrapper.CVDistD_HC                 4.645  1.709   7.461
mvImage                            5.851  0.294   7.687
* 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 
 68.808   2.702  81.411 

Example timings

DAPAR.Rcheck/DAPAR-Ex.timings

nameusersystemelapsed
AggregateMetacell1.0500.0391.257
BuildAdjacencyMatrix0.8600.0290.985
BuildColumnToProteinDataset1.0810.0211.193
BuildMetaCell1.9500.0442.179
CVDistD_HC6.2130.2897.006
Children0.0100.0010.011
CountPep0.8590.0180.882
ExtendPalette0.0560.0020.059
GOAnalysisSave0.0000.0000.001
GetCC3.1690.0673.241
GetColorsForConditions0.7810.0170.808
GetDetailedNbPeptides0.8650.0180.931
GetDetailedNbPeptidesUsed0.0010.0010.001
GetIndices_BasedOnConditions0.8340.0180.906
GetIndices_MetacellFiltering0.8510.0190.890
GetIndices_WholeLine0.8330.0190.875
GetIndices_WholeMatrix0.8430.0241.076
GetKeyId0.8050.0190.999
GetMatAdj0.9350.0221.033
GetMetacell0.0010.0000.001
GetMetacellTags0.8430.0210.921
GetNbPeptidesUsed0.8370.0220.931
GetNbTags000
GetSoftAvailables0.0010.0010.001
GetTypeofData0.7960.0200.855
Get_AllComparisons0.5190.0290.573
GlobalQuantileAlignment0.8320.0180.891
GraphPepProt0.8440.0180.891
LH00.0000.0000.001
LH0.lm0.0000.0000.001
LH10.0000.0010.001
LH1.lm0.0000.0010.002
LOESS2.0410.0432.216
MeanCentering0.8100.0200.885
MetaCellFiltering1.1850.0221.275
MetacellFilteringScope000
Metacell_DIA_NN0.8480.0230.931
Metacell_generic0.8080.0310.902
Metacell_maxquant0.7630.0180.848
Metacell_proline0.7720.0240.828
NumericalFiltering0.9460.0261.006
NumericalgetIndicesOfLinesToRemove0.8250.0170.857
OWAnova0.0110.0010.012
QuantileCentering0.8010.0150.839
SetCC2.8710.0283.025
SetMatAdj0.9140.0180.990
Set_POV_MEC_tags0.8340.0230.948
StringBasedFiltering0.8900.0200.988
StringBasedFiltering20.8870.0200.960
SumByColumns3.7600.2284.264
SymFilteringOperators0.0010.0010.001
UpdateMetacellAfterImputation0.8480.0170.913
aggregateIter1.1830.0221.304
aggregateIterParallel0.0000.0010.001
aggregateMean1.0140.0201.138
aggregateSum1.0830.0211.185
aggregateTopn0.9910.0191.056
applyAnovasOnProteins0.2390.0150.265
averageIntensities1.1390.2371.622
barplotEnrichGO_HC15.121 3.02119.940
barplotGroupGO_HC 8.911 1.22010.758
boxPlotD_HC0.5140.1530.787
buildGraph2.2080.0712.434
check.conditions0.7820.0170.825
check.design0.7950.0180.924
checkClusterability 6.249 3.57910.287
classic1wayAnova0.0000.0000.001
compareNormalizationD_HC0.3040.0990.411
compute.selection.table1.4750.2561.848
compute_t_tests2.4440.3513.125
corrMatrixD_HC0.9820.1251.221
createMSnset3.2690.1533.957
createMSnset23.1730.1513.802
dapar_hc_ExportMenu0.2720.2480.599
dapar_hc_chart0.1040.0830.216
deleteLinesFromIndices0.8950.0421.059
densityPlotD_HC6.3952.5159.501
diffAnaComputeAdjustedPValues0.3980.0760.569
diffAnaComputeFDR0.0010.0000.000
diffAnaGetSignificant0.5450.1060.818
diffAnaSave0.5190.0960.731
diffAnaVolcanoplot0.3380.0530.456
diffAnaVolcanoplot_rCharts0.7480.2031.124
display.CC.visNet2.4070.1492.850
enrich_GO 8.818 1.02711.332
finalizeAggregation0.0000.0010.001
findMECBlock0.8830.0331.063
formatHSDResults0.0000.0000.001
formatLimmaResult0.3320.0500.418
formatPHResults0.0000.0010.000
formatPHTResults0.0000.0010.000
fudge2LRT0.0000.0010.001
get.pep.prot.cc2.1500.0502.536
getDesignLevel0.7930.0180.928
getIndicesConditions0.7930.0160.898
getIndicesOfLinesToRemove0.8280.0290.973
getListNbValuesInLines0.7890.0160.864
getNumberOf0.8320.0291.011
getNumberOfEmptyLines0.8610.0221.048
getPourcentageOfMV0.8460.0321.099
getProcessingInfo0.7850.0170.915
getProteinsStats0.8590.0331.067
getQuantile4Imp0.1880.0160.239
getTextForAggregation0.0000.0000.001
getTextForAnaDiff0.0010.0000.001
getTextForFiltering000
getTextForGOAnalysis0.0010.0000.001
getTextForHypothesisTest0.0000.0000.001
getTextForNewDataset0.0040.0010.005
getTextForNormalization000
getTextForpeptideImputation0.0010.0000.001
getTextForproteinImputation0.0000.0000.001
globalAdjPval0.9850.0941.437
group_GO 8.813 1.03411.319
hc_logFC_DensityPlot1.4330.5602.270
hc_mvTypePlot21.8730.5152.839
heatmapD1.3030.1061.703
heatmapForMissingValues0.3520.0500.486
histPValue_HC0.4580.1420.765
impute.pa20.9250.0551.156
inner.aggregate.iter0.9230.0491.127
inner.aggregate.topn0.8760.0341.181
inner.mean0.8690.0331.104
inner.sum0.9220.0361.119
is.subset0.0010.0010.002
limmaCompleteTest3.6150.1194.466
listSheets0.0000.0000.001
make.contrast0.8210.0200.976
make.design.10.8230.0180.967
make.design.20.8270.0200.977
make.design.30.8220.0200.967
make.design0.8670.0211.033
match.metacell0.8730.0321.132
metacell.def0.0110.0060.016
metacellHisto_HC0.9250.1091.241
metacellPerLinesHistoPerCondition_HC1.1630.1981.630
metacellPerLinesHisto_HC1.4220.4662.373
metacombine0.4730.0250.597
mvImage5.8510.2947.687
my_hc_ExportMenu0.2830.2470.707
my_hc_chart0.2830.2510.729
nonzero0.0290.0020.043
normalizeMethods.dapar0.0010.0010.001
pepa.test0.8690.0341.098
pkgs.require000
plotJitter2.2550.0752.724
plotJitter_rCharts2.2170.1422.829
plotPCA_Eigen0.9780.0751.261
plotPCA_Eigen_hc0.7940.0160.954
plotPCA_Ind0.8090.0221.080
plotPCA_Var0.7940.0170.917
postHocTest000
proportionConRev_HC0.1030.0850.273
rbindMSnset1.0000.0731.281
reIntroduceMEC0.9270.0511.169
readExcel0.0000.0010.001
removeLines0.8890.0491.091
samLRT000
saveParameters0.7970.0190.953
scatterplotEnrichGO_HC 8.687 0.99711.942
search.metacell.tags0.0160.0040.019
separateAdjPval0.3360.0320.487
splitAdjacencyMat0.8660.0311.160
test.design0.8220.0181.003
testAnovaModels0.2490.0300.401
thresholdpval4fdr0.0010.0000.000
translatedRandomBeta0.0050.0140.019
univ_AnnotDbPkg0.3300.1420.596
violinPlotD0.6030.0500.946
visualizeClusters3.1550.4094.696
vsn1.2460.0361.569
wrapper.CVDistD_HC4.6451.7097.461
wrapper.compareNormalizationD_HC107.085 46.271176.049
wrapper.corrMatrixD_HC0.9900.1431.469
wrapper.dapar.impute.mi30.725 1.71539.687
wrapper.heatmapD1.1660.0811.501
wrapper.impute.KNN0.8860.0441.098
wrapper.impute.detQuant1.0160.0711.325
wrapper.impute.fixedValue0.9680.0691.158
wrapper.impute.mle0.8870.0451.100
wrapper.impute.pa0.2830.0420.408
wrapper.impute.pa20.9110.0571.116
wrapper.impute.slsa1.2050.0831.363
wrapper.mvImage0.3370.0620.582
wrapper.normalizeD0.8740.0260.993
wrapper.pca0.3250.0530.453
wrapperCalibrationPlot0.3830.0630.592
wrapperClassic1wayAnova000
wrapperRunClustering6.2080.7477.955
write.excel1.6350.2582.147
writeMSnsetToCSV0.8430.0500.997
writeMSnsetToExcel2.1330.4193.055