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This page was generated on 2024-06-28 17:39 -0400 (Fri, 28 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4760
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4494
merida1macOS 12.7.4 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4508
kjohnson1macOS 13.6.6 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4466
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4362
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 509/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DAPAR 1.36.2  (landing page)
Samuel Wieczorek
Snapshot Date: 2024-06-26 14:00 -0400 (Wed, 26 Jun 2024)
git_url: https://git.bioconductor.org/packages/DAPAR
git_branch: RELEASE_3_19
git_last_commit: 34a0be9
git_last_commit_date: 2024-06-10 09:45:54 -0400 (Mon, 10 Jun 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows 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
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  


CHECK results for DAPAR on nebbiolo1

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: 1.36.2
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:DAPAR.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings DAPAR_1.36.2.tar.gz
StartedAt: 2024-06-26 22:16:05 -0400 (Wed, 26 Jun 2024)
EndedAt: 2024-06-26 22:24:05 -0400 (Wed, 26 Jun 2024)
EllapsedTime: 479.9 seconds
RetCode: 0
Status:   OK  
CheckDir: DAPAR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:DAPAR.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings DAPAR_1.36.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/DAPAR.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘DAPAR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DAPAR’ version ‘1.36.2’
* 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 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 33.338  9.123  43.134
wrapper.dapar.impute.mi          12.626  0.360  13.000
barplotEnrichGO_HC                7.721  0.989   8.735
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/DAPAR.Rcheck/00check.log’
for details.


Installation output

DAPAR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL DAPAR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-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 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 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 1.36.2.

  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 
 30.029   1.922  31.942 

Example timings

DAPAR.Rcheck/DAPAR-Ex.timings

nameusersystemelapsed
AggregateMetacell0.5470.0210.569
BuildAdjacencyMatrix1.2730.2441.517
BuildColumnToProteinDataset0.4860.0240.509
BuildMetaCell0.5310.0520.585
CVDistD_HC2.0690.1912.275
Children0.0040.0000.004
CountPep0.4600.0280.488
ExtendPalette0.0290.0000.028
GOAnalysisSave000
GetCC2.8780.2323.109
GetColorsForConditions0.4240.0110.437
GetDetailedNbPeptides0.4370.0190.456
GetDetailedNbPeptidesUsed000
GetIndices_BasedOnConditions0.4280.0280.456
GetIndices_MetacellFiltering0.4480.0080.456
GetIndices_WholeLine0.4360.0160.453
GetIndices_WholeMatrix0.4300.0320.462
GetKeyId0.4240.0110.437
GetMatAdj0.4610.0290.489
GetMetacell0.0000.0000.001
GetMetacellTags0.4340.0120.445
GetNbPeptidesUsed0.4280.0240.451
GetNbTags000
GetSoftAvailables000
GetTypeofData0.4220.0110.434
Get_AllComparisons0.2410.0280.270
GlobalQuantileAlignment0.4700.0200.491
GraphPepProt0.4310.0200.451
LH0000
LH0.lm000
LH1000
LH1.lm0.0000.0000.001
LOESS1.1140.0331.147
MeanCentering0.4290.0200.449
MetaCellFiltering0.6200.0270.646
MetacellFilteringScope0.0010.0000.000
Metacell_DIA_NN0.4920.0000.492
Metacell_generic0.3890.0040.393
Metacell_maxquant0.4400.0080.448
Metacell_proline0.3860.0080.393
NumericalFiltering0.4520.0160.468
NumericalgetIndicesOfLinesToRemove0.4110.0200.431
OWAnova0.0080.0000.008
QuantileCentering0.420.000.42
SetCC2.1010.1922.293
SetMatAdj0.4410.0160.457
Set_POV_MEC_tags0.4260.0080.434
StringBasedFiltering0.4460.0120.458
StringBasedFiltering20.4460.0120.457
SumByColumns1.2120.0281.240
SymFilteringOperators000
UpdateMetacellAfterImputation0.4330.0200.453
aggregateIter0.5580.0080.567
aggregateIterParallel0.0000.0010.000
aggregateMean0.5090.0150.524
aggregateSum0.5130.0160.529
aggregateTopn0.4820.0080.490
applyAnovasOnProteins0.1310.0040.135
averageIntensities0.4350.0890.525
barplotEnrichGO_HC7.7210.9898.735
barplotGroupGO_HC4.6060.2134.826
boxPlotD_HC0.2950.0160.312
buildGraph1.4850.0761.561
check.conditions0.4210.0040.424
check.design0.4150.0080.422
checkClusterability2.5400.6733.266
classic1wayAnova000
compareNormalizationD_HC0.1610.0160.177
compute.selection.table0.6440.0320.679
compute_t_tests0.9400.0661.009
corrMatrixD_HC0.5560.0480.604
createMSnset1.5190.0681.587
createMSnset21.5400.0441.585
dapar_hc_ExportMenu0.1040.0360.142
dapar_hc_chart0.0510.0080.059
deleteLinesFromIndices0.4460.0240.470
densityPlotD_HC2.2580.4922.784
diffAnaComputeAdjustedPValues0.1690.0220.192
diffAnaComputeFDR000
diffAnaGetSignificant0.2560.0210.278
diffAnaSave0.2390.0160.255
diffAnaVolcanoplot0.1750.0090.183
diffAnaVolcanoplot_rCharts0.3570.0320.391
display.CC.visNet1.6690.1441.813
enrich_GO4.2950.2064.508
finalizeAggregation000
findMECBlock0.4380.0400.478
formatHSDResults000
formatLimmaResult0.1660.0080.174
formatPHResults000
formatPHTResults0.0010.0000.000
fudge2LRT0.0000.0000.001
get.pep.prot.cc1.4640.0601.524
getDesignLevel0.4190.0000.420
getIndicesConditions0.420.000.42
getIndicesOfLinesToRemove0.4280.0070.435
getListNbValuesInLines0.4170.0040.422
getNumberOf0.4370.0200.457
getNumberOfEmptyLines0.4500.0160.466
getPourcentageOfMV0.4440.0120.457
getProcessingInfo0.4140.0080.423
getProteinsStats0.4380.0160.454
getQuantile4Imp0.1130.0040.116
getTextForAggregation000
getTextForAnaDiff000
getTextForFiltering000
getTextForGOAnalysis000
getTextForHypothesisTest000
getTextForNewDataset0.0010.0010.002
getTextForNormalization0.0000.0000.001
getTextForpeptideImputation0.0000.0000.001
getTextForproteinImputation0.0000.0000.001
globalAdjPval0.4080.0080.417
group_GO4.2600.1804.448
hc_logFC_DensityPlot0.4860.1050.596
hc_mvTypePlot20.8830.1731.061
heatmapD0.8050.0240.828
heatmapForMissingValues0.1790.0240.203
histPValue_HC0.2130.0160.230
impute.pa20.4670.0200.487
inner.aggregate.iter0.4590.0360.496
inner.aggregate.topn0.4640.0200.484
inner.mean0.4470.0240.471
inner.sum0.5030.0040.507
is.subset0.0000.0000.001
limmaCompleteTest1.2450.0401.287
listSheets0.0000.0000.001
make.contrast0.4260.0190.447
make.design.10.4440.0090.454
make.design.20.4390.0170.456
make.design.30.4490.0120.461
make.design0.4300.0160.446
match.metacell0.6340.0280.663
metacell.def0.0000.0040.005
metacellHisto_HC0.4800.0200.501
metacellPerLinesHistoPerCondition_HC0.5760.0400.616
metacellPerLinesHisto_HC0.6630.0480.712
metacombine0.0490.0000.050
mvImage1.8850.0401.926
my_hc_ExportMenu0.1090.0280.137
my_hc_chart0.1090.0240.133
nonzero0.0150.0000.015
normalizeMethods.dapar000
pepa.test0.4230.0310.454
pkgs.require0.0000.0000.001
plotJitter1.4710.1041.576
plotJitter_rCharts1.3920.0761.469
plotPCA_Eigen0.4570.0280.486
plotPCA_Eigen_hc0.4040.0120.416
plotPCA_Ind0.4110.0120.423
plotPCA_Var0.4150.0000.415
postHocTest0.0010.0000.001
proportionConRev_HC0.0420.0040.046
rbindMSnset0.4580.0360.495
reIntroduceMEC0.4540.0160.471
readExcel000
removeLines0.4390.0160.455
samLRT000
saveParameters0.400.020.42
scatterplotEnrichGO_HC4.2130.1904.410
search.metacell.tags0.0030.0030.006
separateAdjPval0.1840.0080.192
splitAdjacencyMat0.4460.0160.463
test.design0.4330.0070.441
testAnovaModels0.1390.0040.143
thresholdpval4fdr000
translatedRandomBeta0.0000.0080.008
univ_AnnotDbPkg0.1280.0530.179
violinPlotD0.3950.0090.404
visualizeClusters1.0540.0451.100
vsn0.6660.0080.674
wrapper.CVDistD_HC1.4950.2871.802
wrapper.compareNormalizationD_HC33.338 9.12343.134
wrapper.corrMatrixD_HC0.4940.0230.517
wrapper.dapar.impute.mi12.626 0.36013.000
wrapper.heatmapD0.6450.0190.664
wrapper.impute.KNN0.4710.0150.486
wrapper.impute.detQuant0.4640.0160.481
wrapper.impute.fixedValue0.4610.0240.486
wrapper.impute.mle0.4440.0160.460
wrapper.impute.pa0.1350.0200.155
wrapper.impute.pa20.4420.0160.458
wrapper.impute.slsa0.5530.0230.577
wrapper.mvImage0.1500.0210.172
wrapper.normalizeD0.4210.0080.429
wrapper.pca0.1570.0080.164
wrapperCalibrationPlot0.1890.0190.209
wrapperClassic1wayAnova0.0000.0010.000
wrapperRunClustering1.8300.1221.960
write.excel0.7360.0530.791
writeMSnsetToCSV0.4540.0090.463
writeMSnsetToExcel0.8740.0920.970