Back to Multiple platform build/check report for BioC 3.20:   simplified   long
ABC[D]EFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2024-06-11 15:41 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4679
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4414
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4441
kjohnson1macOS 13.6.6 Venturaarm644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4394
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 494/2239HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DAPAR 1.37.0  (landing page)
Samuel Wieczorek
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/DAPAR
git_branch: devel
git_last_commit: a0803ea
git_last_commit_date: 2024-04-30 10:45:58 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 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


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: 1.37.0
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_1.37.0.tar.gz
StartedAt: 2024-06-10 02:17:46 -0400 (Mon, 10 Jun 2024)
EndedAt: 2024-06-10 02:38:38 -0400 (Mon, 10 Jun 2024)
EllapsedTime: 1251.1 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_1.37.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/DAPAR.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* 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 12.7.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DAPAR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DAPAR’ version ‘1.37.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 111.104 46.566 177.233
wrapper.dapar.impute.mi           33.633  1.774  43.167
barplotEnrichGO_HC                16.842  3.538  27.850
barplotGroupGO_HC                 10.087  1.351  15.201
checkClusterability                7.254  3.861  12.644
enrich_GO                          9.559  1.113  13.510
scatterplotEnrichGO_HC             9.537  1.099  13.699
group_GO                           9.522  1.111  13.413
densityPlotD_HC                    6.528  2.927  10.497
CVDistD_HC                         6.550  0.523  18.674
wrapper.CVDistD_HC                 4.617  1.784   7.386
mvImage                            5.674  0.302   7.593
wrapperRunClustering               4.793  0.661   6.956
* 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-3.20-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 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"
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 1.37.0.

  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 18 | SKIP 0 | PASS 66 ]

[ FAIL 0 | WARN 18 | SKIP 0 | PASS 66 ]
> 
> proc.time()
   user  system elapsed 
 63.197   2.344  89.231 

Example timings

DAPAR.Rcheck/DAPAR-Ex.timings

nameusersystemelapsed
AggregateMetacell0.7160.0192.051
BuildAdjacencyMatrix1.4520.0311.714
BuildColumnToProteinDataset0.7000.0171.106
BuildMetaCell1.0390.0632.544
CVDistD_HC 6.550 0.52318.674
Children0.0120.0020.014
CountPep0.5800.0150.726
ExtendPalette0.0660.0050.102
GOAnalysisSave0.0000.0000.001
GetCC3.7080.0594.278
GetColorsForConditions0.4790.0080.548
GetDetailedNbPeptides0.5280.0080.580
GetDetailedNbPeptidesUsed0.0010.0010.001
GetIndices_BasedOnConditions0.5180.0100.605
GetIndices_MetacellFiltering0.5430.0130.673
GetIndices_WholeLine0.5170.0110.596
GetIndices_WholeMatrix0.5020.0120.559
GetKeyId0.4750.0090.556
GetMatAdj0.6060.0090.657
GetMetacell0.0000.0000.001
GetMetacellTags0.5090.0100.540
GetNbPeptidesUsed0.5220.0120.600
GetNbTags0.0000.0010.000
GetSoftAvailables0.0010.0010.001
GetTypeofData0.4750.0120.567
Get_AllComparisons0.4320.0120.571
GlobalQuantileAlignment0.5430.0220.681
GraphPepProt0.5190.0110.621
LH00.0000.0010.001
LH0.lm0.0000.0000.001
LH10.0000.0010.001
LH1.lm0.0000.0010.000
LOESS1.6880.0261.928
MeanCentering0.4930.0160.582
MetaCellFiltering0.9210.0261.145
MetacellFilteringScope0.0000.0010.001
Metacell_DIA_NN0.8740.0211.063
Metacell_generic0.7880.0231.018
Metacell_maxquant0.8230.0291.038
Metacell_proline0.7760.0180.937
NumericalFiltering0.5790.0090.730
NumericalgetIndicesOfLinesToRemove0.4900.0060.618
OWAnova0.0120.0020.022
QuantileCentering0.4690.0070.576
SetCC2.5340.0323.115
SetMatAdj0.5910.0130.771
Set_POV_MEC_tags0.5130.0080.638
StringBasedFiltering0.5760.0120.730
StringBasedFiltering20.5660.0090.708
SumByColumns3.5390.0544.236
SymFilteringOperators0.0000.0000.001
UpdateMetacellAfterImputation0.5360.0110.636
aggregateIter0.8610.0141.052
aggregateIterParallel000
aggregateMean0.7230.0100.841
aggregateSum0.7280.0091.145
aggregateTopn0.6560.0100.866
applyAnovasOnProteins0.1540.0060.214
averageIntensities1.0630.2471.788
barplotEnrichGO_HC16.842 3.53827.850
barplotGroupGO_HC10.087 1.35115.201
boxPlotD_HC0.5240.1710.915
buildGraph1.9180.0582.389
check.conditions0.4590.0060.538
check.design0.4630.0080.572
checkClusterability 7.254 3.86112.644
classic1wayAnova0.0000.0000.001
compareNormalizationD_HC0.2250.0990.432
compute.selection.table1.4910.2532.279
compute_t_tests2.5840.4363.842
corrMatrixD_HC0.7600.1621.188
createMSnset3.2370.2224.553
createMSnset23.1880.2004.310
dapar_hc_ExportMenu0.2800.2570.672
dapar_hc_chart0.1160.0850.237
deleteLinesFromIndices0.5660.0420.814
densityPlotD_HC 6.528 2.92710.497
diffAnaComputeAdjustedPValues0.2800.0760.516
diffAnaComputeFDR0.0000.0010.001
diffAnaGetSignificant0.5030.1150.757
diffAnaSave0.4610.1030.704
diffAnaVolcanoplot0.2720.0580.400
diffAnaVolcanoplot_rCharts0.7970.2401.321
display.CC.visNet2.1120.1972.907
enrich_GO 9.559 1.11313.510
finalizeAggregation0.0000.0010.000
findMECBlock0.5480.0230.685
formatHSDResults0.0000.0000.001
formatLimmaResult0.2520.0440.368
formatPHResults0.0000.0010.001
formatPHTResults0.0000.0010.000
fudge2LRT0.0000.0010.000
get.pep.prot.cc1.7880.0532.360
getDesignLevel0.4610.0070.611
getIndicesConditions0.4520.0070.540
getIndicesOfLinesToRemove0.5090.0220.683
getListNbValuesInLines0.4630.0090.564
getNumberOf0.5100.0210.665
getNumberOfEmptyLines0.5420.0130.723
getPourcentageOfMV0.5170.0200.652
getProcessingInfo0.4590.0070.565
getProteinsStats0.5310.0240.702
getQuantile4Imp0.0980.0040.133
getTextForAggregation0.0000.0000.001
getTextForAnaDiff0.0010.0010.002
getTextForFiltering0.0010.0000.001
getTextForGOAnalysis0.0000.0000.001
getTextForHypothesisTest0.0010.0000.001
getTextForNewDataset0.0040.0010.011
getTextForNormalization0.0000.0000.001
getTextForpeptideImputation0.0010.0000.001
getTextForproteinImputation0.0000.0000.001
globalAdjPval0.9120.0811.253
group_GO 9.522 1.11113.413
hc_logFC_DensityPlot1.2810.5272.157
hc_mvTypePlot21.5980.5052.551
heatmapD1.0750.0991.469
heatmapForMissingValues0.2750.0410.490
histPValue_HC0.3760.1320.646
impute.pa20.6000.0430.779
inner.aggregate.iter0.6130.0410.838
inner.aggregate.topn0.5560.0250.702
inner.mean0.5420.0240.712
inner.sum0.6030.0260.755
is.subset0.0010.0010.002
limmaCompleteTest3.4020.1064.290
listSheets0.0000.0000.001
make.contrast0.4880.0070.622
make.design.10.4880.0080.612
make.design.20.4960.0090.633
make.design.30.4950.0100.659
make.design0.4930.0080.687
match.metacell0.7420.0520.984
metacell.def0.0120.0050.017
metacellHisto_HC0.6060.0950.860
metacellPerLinesHistoPerCondition_HC0.8270.1851.255
metacellPerLinesHisto_HC1.1180.4532.076
metacombine0.1710.0120.184
mvImage5.6740.3027.593
my_hc_ExportMenu0.2910.2530.674
my_hc_chart0.2900.2490.709
nonzero0.0300.0030.045
normalizeMethods.dapar0.0010.0010.001
pepa.test0.5410.0210.692
pkgs.require0.0010.0010.001
plotJitter1.9330.0632.570
plotJitter_rCharts1.8820.1862.601
plotPCA_Eigen0.6540.0680.989
plotPCA_Eigen_hc0.4650.0070.571
plotPCA_Ind0.4740.0090.656
plotPCA_Var0.4570.0070.572
postHocTest0.0000.0000.001
proportionConRev_HC0.1030.0830.259
rbindMSnset0.6790.0680.973
reIntroduceMEC0.6020.0410.801
readExcel0.0000.0010.001
removeLines0.5670.0380.779
samLRT0.0000.0000.001
saveParameters0.4670.0090.653
scatterplotEnrichGO_HC 9.537 1.09913.699
search.metacell.tags0.0170.0040.022
separateAdjPval0.2610.0260.464
splitAdjacencyMat0.5370.0230.689
test.design0.4910.0080.619
testAnovaModels0.1690.0210.281
thresholdpval4fdr000
translatedRandomBeta0.0060.0250.032
univ_AnnotDbPkg0.3280.1910.678
violinPlotD0.4360.0320.674
visualizeClusters3.0230.3774.356
vsn0.9470.0251.278
wrapper.CVDistD_HC4.6171.7847.386
wrapper.compareNormalizationD_HC111.104 46.566177.233
wrapper.corrMatrixD_HC0.6800.1191.024
wrapper.dapar.impute.mi33.633 1.77443.167
wrapper.heatmapD0.8550.0701.158
wrapper.impute.KNN0.5610.0330.736
wrapper.impute.detQuant0.6400.0530.862
wrapper.impute.fixedValue0.6540.0570.898
wrapper.impute.mle0.5770.0320.759
wrapper.impute.pa0.2830.0380.393
wrapper.impute.pa20.5930.0440.873
wrapper.impute.slsa0.9360.0701.320
wrapper.mvImage0.2630.0420.373
wrapper.normalizeD0.4950.0090.681
wrapper.pca0.2360.0410.311
wrapperCalibrationPlot0.3010.0510.443
wrapperClassic1wayAnova0.0000.0000.001
wrapperRunClustering4.7930.6616.956
write.excel1.5280.2572.180
writeMSnsetToCSV0.5350.0380.820
writeMSnsetToExcel1.8800.3922.656