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This page was generated on 2025-01-27 12:08 -0500 (Mon, 27 Jan 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4746
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4494
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4517
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4469
taishanLinux (openEuler 24.03 LTS)aarch644.4.2 (2024-10-31) -- "Pile of Leaves" 4395
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: 2025-01-23 13:00 -0500 (Thu, 23 Jan 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 -0500 (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 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: 1.38.0
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_1.38.0.tar.gz
StartedAt: 2025-01-24 02:20:02 -0500 (Fri, 24 Jan 2025)
EndedAt: 2025-01-24 02:43:31 -0500 (Fri, 24 Jan 2025)
EllapsedTime: 1409.7 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_1.38.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/DAPAR.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* 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 ‘1.38.0’
* 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 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 108.877 48.873 187.196
wrapper.dapar.impute.mi           32.208  3.697  47.063
barplotEnrichGO_HC                15.846  7.255  51.085
checkClusterability                7.438  4.307  13.187
barplotGroupGO_HC                  9.068  2.663  22.164
group_GO                           8.555  1.385  15.077
scatterplotEnrichGO_HC             8.652  1.144  11.661
enrich_GO                          8.104  1.433  13.188
densityPlotD_HC                    6.355  2.572  10.304
wrapper.CVDistD_HC                 4.598  1.867   8.035
CVDistD_HC                         5.847  0.400   7.528
mvImage                            5.662  0.377   6.932
wrapperRunClustering               4.486  0.759  12.599
SetCC                              2.733  2.120   7.507
buildGraph                         2.210  2.467   5.583
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-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/4.4-x86_64/Resources/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 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 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 1.38.0.

  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 
 61.557   2.924  95.380 

Example timings

DAPAR.Rcheck/DAPAR-Ex.timings

nameusersystemelapsed
AggregateMetacell0.6550.0401.230
BuildAdjacencyMatrix0.4500.0200.688
BuildColumnToProteinDataset0.5390.0240.922
BuildMetaCell0.9980.0751.682
CVDistD_HC5.8470.4007.528
Children0.0130.0020.016
CountPep1.5570.0321.842
ExtendPalette0.0370.0050.186
GOAnalysisSave0.0000.0010.001
GetCC2.5120.0542.945
GetColorsForConditions0.3640.0230.669
GetDetailedNbPeptides0.5190.0130.597
GetDetailedNbPeptidesUsed0.0000.0000.001
GetIndices_BasedOnConditions0.4670.0200.648
GetIndices_MetacellFiltering0.5300.0220.775
GetIndices_WholeLine0.5220.0110.654
GetIndices_WholeMatrix0.5270.0130.641
GetKeyId0.4800.0140.590
GetMatAdj0.6140.0180.803
GetMetacell000
GetMetacellTags0.5200.0190.684
GetNbPeptidesUsed0.5240.0150.676
GetNbTags0.0000.0010.000
GetSoftAvailables0.0010.0000.002
GetTypeofData0.4840.0140.604
Get_AllComparisons0.4560.0310.589
GlobalQuantileAlignment0.5190.0090.681
GraphPepProt0.5300.0070.643
LH00.0000.0010.000
LH0.lm0.0000.0010.001
LH10.0000.0010.001
LH1.lm0.0000.0010.001
LOESS1.7300.0312.264
MeanCentering0.4650.0430.805
MetaCellFiltering0.6120.0170.743
MetacellFilteringScope0.0000.0000.001
Metacell_DIA_NN0.8220.0741.840
Metacell_generic0.6330.0771.326
Metacell_maxquant0.7380.1021.790
Metacell_proline0.7730.0431.120
NumericalFiltering0.5700.0330.842
NumericalgetIndicesOfLinesToRemove0.5070.0150.666
OWAnova0.0130.0020.018
QuantileCentering0.4860.0140.607
SetCC2.7332.1207.507
SetMatAdj0.6130.0110.703
Set_POV_MEC_tags0.5210.0140.722
StringBasedFiltering0.5790.0120.717
StringBasedFiltering20.5720.0090.645
SumByColumns3.1500.0804.202
SymFilteringOperators0.0000.0010.001
UpdateMetacellAfterImputation0.4610.0300.865
aggregateIter0.8180.0311.156
aggregateIterParallel0.0000.0010.001
aggregateMean0.6720.0190.882
aggregateSum0.7510.0160.993
aggregateTopn0.5420.0330.903
applyAnovasOnProteins0.1550.0080.231
averageIntensities1.0420.5224.543
barplotEnrichGO_HC15.846 7.25551.085
barplotGroupGO_HC 9.068 2.66322.164
boxPlotD_HC0.5140.2621.156
buildGraph2.2102.4675.583
check.conditions0.4600.0140.527
check.design0.4640.0150.568
checkClusterability 7.438 4.30713.187
classic1wayAnova0.0010.0000.000
compareNormalizationD_HC0.2220.1230.486
compute.selection.table1.5130.2902.341
compute_t_tests2.6620.5083.901
corrMatrixD_HC0.7500.1621.147
createMSnset3.2050.2594.663
createMSnset23.1490.2274.347
dapar_hc_ExportMenu0.2870.3091.005
dapar_hc_chart0.1230.0990.313
deleteLinesFromIndices0.5660.0350.727
densityPlotD_HC 6.355 2.57210.304
diffAnaComputeAdjustedPValues0.2640.0690.374
diffAnaComputeFDR000
diffAnaGetSignificant0.4760.0990.729
diffAnaSave0.4410.0880.686
diffAnaVolcanoplot0.2650.0460.379
diffAnaVolcanoplot_rCharts0.6870.2261.815
display.CC.visNet1.8230.1642.751
enrich_GO 8.104 1.43313.188
finalizeAggregation0.0000.0000.001
findMECBlock0.5440.0370.813
formatHSDResults0.0010.0000.001
formatLimmaResult0.2520.0520.387
formatPHResults0.0000.0010.001
formatPHTResults0.0000.0000.001
fudge2LRT0.0000.0010.001
get.pep.prot.cc2.0150.1502.683
getDesignLevel0.4590.0120.634
getIndicesConditions0.4620.0190.623
getIndicesOfLinesToRemove0.3660.0270.555
getListNbValuesInLines0.3130.0200.774
getNumberOf0.4240.0380.791
getNumberOfEmptyLines0.5340.0160.676
getPourcentageOfMV0.5190.0300.743
getProcessingInfo0.4620.0160.625
getProteinsStats0.5330.0430.792
getQuantile4Imp0.0990.0060.152
getTextForAggregation0.0000.0000.001
getTextForAnaDiff0.0010.0010.002
getTextForFiltering0.0000.0010.001
getTextForGOAnalysis0.0010.0010.001
getTextForHypothesisTest0.0000.0000.001
getTextForNewDataset0.0040.0010.005
getTextForNormalization0.0010.0010.002
getTextForpeptideImputation0.0010.0010.001
getTextForproteinImputation0.0000.0000.001
globalAdjPval0.8250.0991.195
group_GO 8.555 1.38515.077
hc_logFC_DensityPlot1.3650.6692.745
hc_mvTypePlot21.7790.6252.961
heatmapD0.9960.1261.447
heatmapForMissingValues0.2670.0460.387
histPValue_HC0.3830.1430.724
impute.pa20.6040.0440.706
inner.aggregate.iter0.6070.0450.728
inner.aggregate.topn0.5540.0270.761
inner.mean0.6060.0390.835
inner.sum0.5410.0260.729
is.subset0.0000.0000.001
limmaCompleteTest3.5190.1494.595
listSheets0.0000.0010.001
make.contrast0.4910.0120.629
make.design.10.4460.0170.609
make.design.20.4340.0180.537
make.design.30.6460.0310.758
make.design0.4850.0090.575
match.metacell0.5420.0210.600
metacell.def0.0130.0060.052
metacellHisto_HC0.6060.1051.409
metacellPerLinesHistoPerCondition_HC0.5230.1971.178
metacellPerLinesHisto_HC1.1240.5012.694
metacombine0.1660.0130.183
mvImage5.6620.3776.932
my_hc_ExportMenu0.2930.2570.889
my_hc_chart0.2840.2440.568
nonzero0.0300.0030.047
normalizeMethods.dapar0.0000.0000.001
pepa.test0.5390.0220.712
pkgs.require0.0000.0010.001
plotJitter2.0470.6343.500
plotJitter_rCharts1.8640.1662.980
plotPCA_Eigen0.6570.0830.949
plotPCA_Eigen_hc0.4700.0080.501
plotPCA_Ind0.4400.0100.503
plotPCA_Var0.4600.0090.561
postHocTest0.0000.0000.001
proportionConRev_HC0.1110.1060.534
rbindMSnset0.6780.0670.852
reIntroduceMEC0.6060.0480.715
readExcel0.0000.0000.001
removeLines0.5690.0430.749
samLRT0.0000.0000.001
saveParameters0.4680.0130.630
scatterplotEnrichGO_HC 8.652 1.14411.661
search.metacell.tags0.0150.0040.020
separateAdjPval0.2600.0260.367
splitAdjacencyMat0.5420.0250.730
test.design0.4990.0080.585
testAnovaModels0.1670.0220.271
thresholdpval4fdr0.0000.0010.000
translatedRandomBeta0.0060.0280.034
univ_AnnotDbPkg0.3030.1800.674
violinPlotD0.6050.0590.840
visualizeClusters2.6040.3863.522
vsn0.9270.0341.119
wrapper.CVDistD_HC4.5981.8678.035
wrapper.compareNormalizationD_HC108.877 48.873187.196
wrapper.corrMatrixD_HC0.7900.1923.726
wrapper.dapar.impute.mi32.208 3.69747.063
wrapper.heatmapD0.7840.0721.064
wrapper.impute.KNN0.5910.0610.722
wrapper.impute.detQuant0.6320.0560.729
wrapper.impute.fixedValue0.6420.0600.742
wrapper.impute.mle0.5250.0340.562
wrapper.impute.pa0.1960.0380.664
wrapper.impute.pa20.5500.0450.687
wrapper.impute.slsa0.8910.0741.113
wrapper.mvImage0.2540.0480.385
wrapper.normalizeD0.4860.0130.546
wrapper.pca0.2310.0450.317
wrapperCalibrationPlot0.2840.0580.653
wrapperClassic1wayAnova0.0000.0010.000
wrapperRunClustering 4.486 0.75912.599
write.excel1.3130.3133.939
writeMSnsetToCSV0.4900.0360.649
writeMSnsetToExcel1.8130.4453.026