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This page was generated on 2025-08-18 12:06 -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 kjohnson3

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: 2025-08-17 18:55:54 -0400 (Sun, 17 Aug 2025)
EndedAt: 2025-08-17 19:00:17 -0400 (Sun, 17 Aug 2025)
EllapsedTime: 263.2 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 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.7
* 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 18.125 11.131  61.511
wrapper.dapar.impute.mi           5.028  0.491   5.964
* 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-arm64/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 Patched (2025-06-14 r88325) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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 
 12.343   0.641  13.032 

Example timings

DAPAR.Rcheck/DAPAR-Ex.timings

nameusersystemelapsed
AggregateMetacell0.2240.0070.247
BuildAdjacencyMatrix0.1940.0020.200
BuildColumnToProteinDataset0.2420.0030.247
BuildMetaCell0.2590.0100.271
CVDistD_HC1.1560.0351.235
Children0.0010.0000.002
CountPep0.2020.0030.214
ExtendPalette0.0090.0010.009
GOAnalysisSave000
GetCC1.0790.0061.163
GetColorsForConditions0.1820.0010.185
GetDetailedNbPeptides0.2090.0010.210
GetDetailedNbPeptidesUsed000
GetIndices_BasedOnConditions0.2110.0020.213
GetIndices_MetacellFiltering0.2100.0020.213
GetIndices_WholeLine0.2130.0030.216
GetIndices_WholeMatrix0.2070.0020.209
GetKeyId0.1870.0010.188
GetMatAdj0.2170.0020.220
GetMetacell000
GetMetacellTags0.1980.0020.201
GetNbPeptidesUsed0.2150.0030.218
GetNbTags000
GetSoftAvailables000
GetTypeofData0.2180.0030.220
Get_AllComparisons0.1250.0050.131
GlobalQuantileAlignment0.2120.0030.214
GraphPepProt0.2070.0020.209
LH0000
LH0.lm000
LH1000
LH1.lm000
LOESS0.5100.0080.521
MeanCentering0.1950.0060.200
MetaCellFiltering0.2600.0030.263
MetacellFilteringScope000
Metacell_DIA_NN0.2130.0070.221
Metacell_generic0.1790.0060.186
Metacell_maxquant0.1960.0080.204
Metacell_proline0.1580.0060.169
NumericalFiltering0.2050.0020.207
NumericalgetIndicesOfLinesToRemove0.1920.0020.193
OWAnova0.0020.0000.003
QuantileCentering0.2090.0040.213
SetCC0.9980.0041.019
SetMatAdj0.1910.0020.193
Set_POV_MEC_tags0.1830.0020.185
StringBasedFiltering0.1950.0020.197
StringBasedFiltering20.1900.0020.191
SumByColumns0.4570.0060.462
SymFilteringOperators000
UpdateMetacellAfterImputation0.1920.0030.195
aggregateIter0.2390.0020.243
aggregateIterParallel000
aggregateMean0.2210.0020.223
aggregateSum0.2250.0020.227
aggregateTopn0.2040.0020.206
applyAnovasOnProteins0.0590.0010.059
averageIntensities0.2290.0350.275
barplotEnrichGO_HC3.0330.4783.755
barplotGroupGO_HC2.2570.2922.853
boxPlotD_HC0.1070.0360.248
buildGraph0.7720.0340.835
check.conditions0.1750.0020.184
check.design0.1900.0020.193
checkClusterability1.7581.0473.074
classic1wayAnova000
compareNormalizationD_HC0.0920.0300.126
compute.selection.table0.4720.0810.591
compute_t_tests0.5660.1250.731
corrMatrixD_HC0.2100.0330.248
createMSnset0.6670.0410.738
createMSnset20.6540.0370.716
dapar_hc_ExportMenu0.0400.0380.085
dapar_hc_chart0.0180.0110.029
deleteLinesFromIndices0.2010.0060.225
densityPlotD_HC1.5640.7202.411
diffAnaComputeAdjustedPValues0.1090.0120.122
diffAnaComputeFDR000
diffAnaGetSignificant0.1580.0210.181
diffAnaSave0.1510.0230.177
diffAnaVolcanoplot0.1070.0110.121
diffAnaVolcanoplot_rCharts0.2310.0540.288
display.CC.visNet0.8180.0281.048
enrich_GO2.6310.2293.191
finalizeAggregation000
findMECBlock0.2460.0060.254
formatHSDResults000
formatLimmaResult0.1000.0110.118
formatPHResults0.0010.0000.001
formatPHTResults000
fudge2LRT000
get.pep.prot.cc0.7920.0260.823
getDesignLevel0.1750.0020.178
getIndicesConditions0.1950.0020.199
getIndicesOfLinesToRemove0.1910.0040.196
getListNbValuesInLines0.1880.0020.191
getNumberOf0.2010.0060.212
getNumberOfEmptyLines0.2140.0040.229
getPourcentageOfMV0.2160.0050.221
getProcessingInfo0.2080.0030.213
getProteinsStats0.2180.0060.230
getQuantile4Imp0.0640.0010.066
getTextForAggregation0.0010.0000.000
getTextForAnaDiff000
getTextForFiltering0.0010.0000.001
getTextForGOAnalysis000
getTextForHypothesisTest000
getTextForNewDataset0.0010.0000.002
getTextForNormalization0.0000.0000.001
getTextForpeptideImputation000
getTextForproteinImputation000
globalAdjPval0.2720.0180.303
group_GO2.4200.2243.158
hc_logFC_DensityPlot0.2190.1001.246
hc_mvTypePlot20.9170.0941.452
heatmapD0.2880.0180.345
heatmapForMissingValues0.1170.0110.131
histPValue_HC0.1380.0370.183
impute.pa20.2310.0100.245
inner.aggregate.iter0.2440.0100.260
inner.aggregate.topn0.2170.0080.231
inner.mean0.2070.0060.240
inner.sum0.2080.0070.217
is.subset0.0010.0010.001
limmaCompleteTest0.8800.0310.937
listSheets000
make.contrast0.1960.0030.198
make.design.10.2090.0030.214
make.design.20.1960.0030.206
make.design.30.1930.0040.196
make.design0.1920.0030.195
match.metacell0.2250.0060.231
metacell.def0.0030.0020.005
metacellHisto_HC0.2490.0300.283
metacellPerLinesHistoPerCondition_HC0.3080.0640.397
metacellPerLinesHisto_HC0.3790.1500.584
metacombine0.1260.0050.134
mvImage1.3560.0721.462
my_hc_ExportMenu0.0720.0790.167
my_hc_chart0.0780.0780.174
nonzero0.0170.0010.018
normalizeMethods.dapar000
pepa.test0.2160.0050.229
pkgs.require0.0000.0000.001
plotJitter0.7710.0340.856
plotJitter_rCharts0.7520.0310.923
plotPCA_Eigen0.2110.0120.289
plotPCA_Eigen_hc0.1950.0020.199
plotPCA_Ind0.2260.0040.232
plotPCA_Var0.1960.0030.203
postHocTest000
proportionConRev_HC0.0310.0270.062
rbindMSnset0.2560.0200.292
reIntroduceMEC0.2380.0110.252
readExcel000
removeLines0.2120.0120.232
samLRT000
saveParameters0.2030.0050.217
scatterplotEnrichGO_HC2.3310.2573.619
search.metacell.tags0.0020.0000.017
separateAdjPval0.0820.0040.091
splitAdjacencyMat0.2140.0060.226
test.design0.2200.0040.227
testAnovaModels0.0830.0050.090
thresholdpval4fdr000
translatedRandomBeta0.0020.0040.005
univ_AnnotDbPkg0.1570.0370.201
violinPlotD0.2190.0130.249
visualizeClusters0.8140.0940.937
vsn0.4060.0140.435
wrapper.CVDistD_HC1.1190.4701.598
wrapper.compareNormalizationD_HC18.12511.13161.511
wrapper.corrMatrixD_HC0.2050.0200.245
wrapper.dapar.impute.mi5.0280.4915.964
wrapper.heatmapD0.2780.0150.295
wrapper.impute.KNN0.2210.0110.234
wrapper.impute.detQuant0.2210.0140.238
wrapper.impute.fixedValue0.2290.0120.240
wrapper.impute.mle0.2090.0060.219
wrapper.impute.pa0.0760.0090.088
wrapper.impute.pa20.2130.0100.224
wrapper.impute.slsa0.2890.0160.305
wrapper.mvImage0.0930.0100.105
wrapper.normalizeD0.2090.0050.215
wrapper.pca0.0780.0130.095
wrapperCalibrationPlot0.0890.0140.108
wrapperClassic1wayAnova000
wrapperRunClustering0.6220.1730.855
write.excel0.2950.0450.392
writeMSnsetToCSV0.1880.0100.201
writeMSnsetToExcel0.3520.1290.521