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This page was generated on 2025-08-09 12:09 -0400 (Sat, 09 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4818
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4553
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4595
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4537
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: 2025-08-08 13:45 -0400 (Fri, 08 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 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    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 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


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: 2025-08-08 18:59:24 -0400 (Fri, 08 Aug 2025)
EndedAt: 2025-08-08 19:03:40 -0400 (Fri, 08 Aug 2025)
EllapsedTime: 256.1 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 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 13.7.1
* 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 19.302 11.722  51.303
wrapper.dapar.impute.mi           4.982  0.610   6.170
barplotEnrichGO_HC                3.579  0.564   5.803
* 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 
 12.541   0.713  13.334 

Example timings

DAPAR.Rcheck/DAPAR-Ex.timings

nameusersystemelapsed
AggregateMetacell0.2280.0080.243
BuildAdjacencyMatrix0.1950.0030.199
BuildColumnToProteinDataset0.2260.0030.230
BuildMetaCell0.2830.0110.296
CVDistD_HC1.1730.0341.240
Children0.0020.0000.001
CountPep0.1980.0030.210
ExtendPalette0.0080.0000.008
GOAnalysisSave000
GetCC1.0730.0081.087
GetColorsForConditions0.1820.0020.192
GetDetailedNbPeptides0.1870.0010.196
GetDetailedNbPeptidesUsed000
GetIndices_BasedOnConditions0.1870.0020.189
GetIndices_MetacellFiltering0.1970.0020.200
GetIndices_WholeLine0.2000.0020.201
GetIndices_WholeMatrix0.1970.0020.201
GetKeyId0.1850.0020.187
GetMatAdj0.2130.0030.216
GetMetacell000
GetMetacellTags0.2030.0030.208
GetNbPeptidesUsed0.2060.0020.210
GetNbTags000
GetSoftAvailables000
GetTypeofData0.1810.0020.190
Get_AllComparisons0.1110.0060.121
GlobalQuantileAlignment0.2000.0030.202
GraphPepProt0.2050.0030.208
LH0000
LH0.lm000
LH1000
LH1.lm000
LOESS0.4920.0090.505
MeanCentering0.1900.0040.199
MetaCellFiltering0.2280.0030.230
MetacellFilteringScope000
Metacell_DIA_NN0.2110.0050.224
Metacell_generic0.1660.0050.174
Metacell_maxquant0.1780.0060.186
Metacell_proline0.1650.0050.171
NumericalFiltering0.1920.0020.194
NumericalgetIndicesOfLinesToRemove0.1900.0020.191
OWAnova0.0020.0000.002
QuantileCentering0.1970.0050.202
SetCC1.0040.0051.020
SetMatAdj0.1920.0020.197
Set_POV_MEC_tags0.2030.0030.207
StringBasedFiltering0.1930.0020.194
StringBasedFiltering20.1900.0020.192
SumByColumns0.4850.0060.498
SymFilteringOperators000
UpdateMetacellAfterImputation0.1930.0020.196
aggregateIter0.2360.0030.238
aggregateIterParallel000
aggregateMean0.2160.0030.219
aggregateSum0.2290.0020.231
aggregateTopn0.2150.0030.218
applyAnovasOnProteins0.0640.0010.064
averageIntensities0.2280.0370.352
barplotEnrichGO_HC3.5790.5645.803
barplotGroupGO_HC2.1080.2572.816
boxPlotD_HC0.1000.0240.126
buildGraph0.7740.0310.812
check.conditions0.1750.0020.178
check.design0.1760.0020.178
checkClusterability1.5331.2223.020
classic1wayAnova0.0000.0010.000
compareNormalizationD_HC0.0710.0190.149
compute.selection.table0.4510.0680.528
compute_t_tests0.6970.1170.849
corrMatrixD_HC0.2680.0330.308
createMSnset0.6720.0430.842
createMSnset20.6470.0430.853
dapar_hc_ExportMenu0.0420.0480.304
dapar_hc_chart0.0180.0160.062
deleteLinesFromIndices0.2240.0070.235
densityPlotD_HC1.7160.7132.555
diffAnaComputeAdjustedPValues0.1150.0160.135
diffAnaComputeFDR000
diffAnaGetSignificant0.1210.0310.468
diffAnaSave0.1510.0230.182
diffAnaVolcanoplot0.1130.0110.130
diffAnaVolcanoplot_rCharts0.2450.0580.326
display.CC.visNet0.8820.0331.094
enrich_GO2.6390.2633.186
finalizeAggregation000
findMECBlock0.2210.0060.270
formatHSDResults000
formatLimmaResult0.1100.0130.128
formatPHResults000
formatPHTResults000
fudge2LRT0.0010.0000.000
get.pep.prot.cc0.8070.0220.833
getDesignLevel0.1790.0020.191
getIndicesConditions0.2020.0020.214
getIndicesOfLinesToRemove0.2260.0050.241
getListNbValuesInLines0.1820.0030.187
getNumberOf0.2000.0060.208
getNumberOfEmptyLines0.2060.0040.212
getPourcentageOfMV0.2000.0060.210
getProcessingInfo0.1830.0030.191
getProteinsStats0.2110.0070.223
getQuantile4Imp0.0580.0020.059
getTextForAggregation000
getTextForAnaDiff000
getTextForFiltering0.0000.0000.001
getTextForGOAnalysis0.0000.0010.000
getTextForHypothesisTest000
getTextForNewDataset0.0010.0000.001
getTextForNormalization0.0000.0000.001
getTextForpeptideImputation000
getTextForproteinImputation000
globalAdjPval0.2730.0240.313
group_GO2.3250.2223.061
hc_logFC_DensityPlot0.1900.0900.654
hc_mvTypePlot20.9110.1341.507
heatmapD0.3070.0270.338
heatmapForMissingValues0.1110.0120.126
histPValue_HC0.1440.0370.186
impute.pa20.2330.0100.252
inner.aggregate.iter0.2320.0090.244
inner.aggregate.topn0.2260.0060.243
inner.mean0.2190.0060.229
inner.sum0.1930.0040.202
is.subset000
limmaCompleteTest0.8060.0330.849
listSheets000
make.contrast0.1960.0040.200
make.design.10.1990.0030.202
make.design.20.2190.0030.225
make.design.30.2210.0030.230
make.design0.2420.0040.250
match.metacell0.2180.0070.233
metacell.def0.0030.0020.004
metacellHisto_HC0.2370.0340.280
metacellPerLinesHistoPerCondition_HC0.3060.0750.409
metacellPerLinesHisto_HC0.3850.1690.746
metacombine0.1280.0060.139
mvImage1.4320.0901.568
my_hc_ExportMenu0.0910.0790.169
my_hc_chart0.0910.0810.172
nonzero0.0180.0010.020
normalizeMethods.dapar000
pepa.test0.2540.0060.261
pkgs.require000
plotJitter0.8560.0330.953
plotJitter_rCharts0.7620.0321.059
plotPCA_Eigen0.2480.0220.280
plotPCA_Eigen_hc0.2320.0020.238
plotPCA_Ind0.2330.0060.251
plotPCA_Var0.2300.0040.242
postHocTest0.0000.0010.000
proportionConRev_HC0.0310.0280.060
rbindMSnset0.2790.0210.308
reIntroduceMEC0.2610.0160.287
readExcel000
removeLines0.2270.0120.252
samLRT000
saveParameters0.2160.0040.223
scatterplotEnrichGO_HC2.6150.3413.539
search.metacell.tags0.0030.0020.006
separateAdjPval0.0960.0120.169
splitAdjacencyMat0.2330.0140.255
test.design0.2130.0050.222
testAnovaModels0.0860.0110.106
thresholdpval4fdr000
translatedRandomBeta0.0010.0040.008
univ_AnnotDbPkg0.1160.0410.170
violinPlotD0.1510.0130.179
visualizeClusters0.4470.1211.515
vsn0.3440.0290.414
wrapper.CVDistD_HC1.280.832.32
wrapper.compareNormalizationD_HC19.30211.72251.303
wrapper.corrMatrixD_HC0.2120.0230.235
wrapper.dapar.impute.mi4.9820.6106.170
wrapper.heatmapD0.2510.0130.280
wrapper.impute.KNN0.2040.0120.261
wrapper.impute.detQuant0.2110.0160.239
wrapper.impute.fixedValue0.2300.0120.242
wrapper.impute.mle0.2120.0100.225
wrapper.impute.pa0.0840.0080.091
wrapper.impute.pa20.2180.0090.226
wrapper.impute.slsa0.3090.0200.336
wrapper.mvImage0.0900.0150.111
wrapper.normalizeD0.1930.0040.198
wrapper.pca0.0930.0100.103
wrapperCalibrationPlot0.1170.0140.132
wrapperClassic1wayAnova0.0000.0010.000
wrapperRunClustering1.2450.2031.517
write.excel0.4150.0720.505
writeMSnsetToCSV0.1980.0130.217
writeMSnsetToExcel0.5330.1020.638