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This page was generated on 2025-03-20 12:05 -0400 (Thu, 20 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.3 (2025-02-28) -- "Trophy Case" 4756
palomino8Windows Server 2022 Datacenterx644.4.3 (2025-02-28 ucrt) -- "Trophy Case" 4487
merida1macOS 12.7.5 Montereyx86_644.4.3 (2025-02-28) -- "Trophy Case" 4514
kjohnson1macOS 13.6.6 Venturaarm644.4.3 (2025-02-28) -- "Trophy Case" 4441
taishanLinux (openEuler 24.03 LTS)aarch644.4.3 (2025-02-28) -- "Trophy Case" 4406
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 504/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DAPAR 1.38.0  (landing page)
Samuel Wieczorek
Snapshot Date: 2025-03-17 13:00 -0400 (Mon, 17 Mar 2025)
git_url: https://git.bioconductor.org/packages/DAPAR
git_branch: RELEASE_3_20
git_last_commit: 62bc537
git_last_commit_date: 2024-10-29 10:04:09 -0400 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 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
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
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: 1.38.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:DAPAR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings DAPAR_1.38.0.tar.gz
StartedAt: 2025-03-17 22:11:32 -0400 (Mon, 17 Mar 2025)
EndedAt: 2025-03-17 22:19:32 -0400 (Mon, 17 Mar 2025)
EllapsedTime: 480.5 seconds
RetCode: 0
Status:   OK  
CheckDir: DAPAR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:DAPAR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings DAPAR_1.38.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/DAPAR.Rcheck’
* using R version 4.4.3 (2025-02-28)
* 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 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘DAPAR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DAPAR’ version ‘1.38.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
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 35.859 12.392  48.591
wrapper.dapar.impute.mi          13.788  0.736  14.538
barplotEnrichGO_HC                7.196  1.090   8.323
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/DAPAR.Rcheck/00check.log’
for details.


Installation output

DAPAR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL DAPAR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘DAPAR’ ...
** 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 4.4.3 (2025-02-28) -- "Trophy Case"
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 1.38.0.

  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 
 33.913   1.143  35.053 

Example timings

DAPAR.Rcheck/DAPAR-Ex.timings

nameusersystemelapsed
AggregateMetacell0.5250.0170.543
BuildAdjacencyMatrix0.4570.0120.469
BuildColumnToProteinDataset0.5130.0080.521
BuildMetaCell0.4880.0160.505
CVDistD_HC2.1480.1202.288
Children0.0040.0000.005
CountPep1.2480.0581.306
ExtendPalette0.0240.0000.023
GOAnalysisSave000
GetCC2.1410.0662.208
GetColorsForConditions0.4380.0160.454
GetDetailedNbPeptides0.4650.0080.472
GetDetailedNbPeptidesUsed000
GetIndices_BasedOnConditions0.4490.0320.481
GetIndices_MetacellFiltering0.4580.0110.470
GetIndices_WholeLine0.4540.0130.467
GetIndices_WholeMatrix0.4510.0120.463
GetKeyId0.4500.0130.463
GetMatAdj0.4820.0160.499
GetMetacell000
GetMetacellTags0.4360.0290.464
GetNbPeptidesUsed0.4390.0210.459
GetNbTags000
GetSoftAvailables0.0000.0000.001
GetTypeofData0.4260.0150.442
Get_AllComparisons0.2640.0420.306
GlobalQuantileAlignment0.4500.0240.475
GraphPepProt0.4540.0160.469
LH0000
LH0.lm000
LH1000
LH1.lm000
LOESS1.1430.0531.196
MeanCentering0.4560.0230.479
MetaCellFiltering0.5750.0160.591
MetacellFilteringScope000
Metacell_DIA_NN0.4240.0030.428
Metacell_generic0.3580.0030.361
Metacell_maxquant0.3880.0040.392
Metacell_proline0.3560.0020.358
NumericalFiltering0.4740.0060.480
NumericalgetIndicesOfLinesToRemove0.4350.0070.443
OWAnova0.0030.0020.006
QuantileCentering0.4320.0040.437
SetCC2.1900.1142.304
SetMatAdj0.4720.0090.480
Set_POV_MEC_tags0.4440.0080.452
StringBasedFiltering0.4650.0110.476
StringBasedFiltering20.4650.0080.473
SumByColumns1.1940.0111.205
SymFilteringOperators000
UpdateMetacellAfterImputation0.4600.0180.478
aggregateIter0.5880.0090.597
aggregateIterParallel000
aggregateMean0.5100.0070.517
aggregateSum0.5260.0220.548
aggregateTopn0.5100.0120.522
applyAnovasOnProteins0.1290.0080.137
averageIntensities0.4780.0310.511
barplotEnrichGO_HC7.1961.0908.323
barplotGroupGO_HC4.1620.5734.744
boxPlotD_HC0.2920.0170.309
buildGraph1.5080.1181.626
check.conditions0.4150.0120.427
check.design0.4200.0110.432
checkClusterability2.6181.0233.667
classic1wayAnova000
compareNormalizationD_HC0.1680.0110.180
compute.selection.table0.6480.0960.747
compute_t_tests0.9640.1431.113
corrMatrixD_HC0.5540.0520.607
createMSnset1.4400.1241.566
createMSnset21.4240.0511.475
dapar_hc_ExportMenu0.1100.0250.136
dapar_hc_chart0.0480.0070.055
deleteLinesFromIndices0.4670.0220.490
densityPlotD_HC2.3750.7943.182
diffAnaComputeAdjustedPValues0.1730.0110.185
diffAnaComputeFDR000
diffAnaGetSignificant0.2430.0190.263
diffAnaSave0.2300.0220.253
diffAnaVolcanoplot0.1710.0130.184
diffAnaVolcanoplot_rCharts0.3260.0440.372
display.CC.visNet1.6040.1891.794
enrich_GO4.0150.2174.238
finalizeAggregation000
findMECBlock0.4590.0210.480
formatHSDResults000
formatLimmaResult0.1720.0070.179
formatPHResults000
formatPHTResults000
fudge2LRT000
get.pep.prot.cc1.5920.1131.705
getDesignLevel0.4270.0090.436
getIndicesConditions0.4250.0060.431
getIndicesOfLinesToRemove0.4440.0120.455
getListNbValuesInLines0.4260.0120.438
getNumberOf0.4310.0250.456
getNumberOfEmptyLines0.4490.0070.457
getPourcentageOfMV0.4440.0180.462
getProcessingInfo0.430.010.44
getProteinsStats0.4440.0200.466
getQuantile4Imp0.1160.0030.119
getTextForAggregation000
getTextForAnaDiff000
getTextForFiltering0.0010.0000.001
getTextForGOAnalysis000
getTextForHypothesisTest0.0010.0000.000
getTextForNewDataset0.0020.0000.002
getTextForNormalization000
getTextForpeptideImputation0.0010.0000.000
getTextForproteinImputation000
globalAdjPval0.3860.0180.404
group_GO4.0870.2004.300
hc_logFC_DensityPlot0.5080.1330.645
hc_mvTypePlot20.8640.1501.017
heatmapD0.6960.0270.723
heatmapForMissingValues0.1970.0080.206
histPValue_HC0.2230.0240.248
impute.pa20.4900.0080.499
inner.aggregate.iter0.4930.0200.514
inner.aggregate.topn0.5140.0090.524
inner.mean0.4640.0120.477
inner.sum0.4700.0080.478
is.subset0.0010.0000.000
limmaCompleteTest1.3040.0301.335
listSheets000
make.contrast0.4430.0110.454
make.design.10.4440.0180.462
make.design.20.5730.0130.586
make.design.30.4430.0100.453
make.design0.4430.0130.455
match.metacell0.4610.0120.473
metacell.def0.0050.0000.005
metacellHisto_HC0.4860.0190.505
metacellPerLinesHistoPerCondition_HC0.5840.0240.609
metacellPerLinesHisto_HC0.6760.0540.732
metacombine0.0500.0020.053
mvImage1.9610.0562.020
my_hc_ExportMenu0.1090.0250.134
my_hc_chart0.1080.0300.138
nonzero0.0160.0010.017
normalizeMethods.dapar000
pepa.test0.4630.0190.483
pkgs.require000
plotJitter1.6600.1341.794
plotJitter_rCharts1.5200.0331.553
plotPCA_Eigen0.4970.0180.516
plotPCA_Eigen_hc0.4250.0080.433
plotPCA_Ind0.4290.0070.437
plotPCA_Var0.4250.0060.431
postHocTest000
proportionConRev_HC0.0390.0060.045
rbindMSnset0.4960.0150.511
reIntroduceMEC0.4580.0210.479
readExcel000
removeLines0.4520.0260.478
samLRT000
saveParameters0.4270.0060.433
scatterplotEnrichGO_HC3.9780.2344.218
search.metacell.tags0.0040.0020.006
separateAdjPval0.2000.0030.203
splitAdjacencyMat0.4790.0100.489
test.design0.4550.0100.465
testAnovaModels0.1380.0070.145
thresholdpval4fdr000
translatedRandomBeta0.0020.0000.002
univ_AnnotDbPkg0.1210.0120.133
violinPlotD0.4140.0050.418
visualizeClusters1.0760.1381.216
vsn0.6720.0220.694
wrapper.CVDistD_HC1.6520.4092.069
wrapper.compareNormalizationD_HC35.85912.39248.591
wrapper.corrMatrixD_HC0.5710.0680.639
wrapper.dapar.impute.mi13.788 0.73614.538
wrapper.heatmapD0.6260.0310.657
wrapper.impute.KNN0.4860.0190.506
wrapper.impute.detQuant0.4780.0150.494
wrapper.impute.fixedValue0.4730.0230.497
wrapper.impute.mle0.4470.0140.461
wrapper.impute.pa0.1480.0210.168
wrapper.impute.pa20.4550.0200.475
wrapper.impute.slsa0.5560.0390.596
wrapper.mvImage0.1660.0190.185
wrapper.normalizeD0.4280.0080.436
wrapper.pca0.1580.0210.179
wrapperCalibrationPlot0.1920.0270.219
wrapperClassic1wayAnova000
wrapperRunClustering1.7930.2532.052
write.excel0.7250.0690.797
writeMSnsetToCSV0.4410.0240.465
writeMSnsetToExcel0.8840.1070.995