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This page was generated on 2024-12-23 12:04 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
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


CHECK results for DAPAR on palomino8

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: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:DAPAR.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings DAPAR_1.38.0.tar.gz
StartedAt: 2024-12-20 00:38:37 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 00:48:23 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 586.7 seconds
RetCode: 0
Status:   OK  
CheckDir: DAPAR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:DAPAR.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings DAPAR_1.38.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/DAPAR.Rcheck'
* using R version 4.4.2 (2024-10-31 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* 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 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 31.63   1.19   33.03
wrapper.dapar.impute.mi          29.78   0.49   30.43
barplotEnrichGO_HC                8.31   0.67   10.36
barplotGroupGO_HC                 4.81   0.34    5.19
CVDistD_HC                        2.91   0.27    9.68
display.CC.visNet                 1.49   0.03    5.12
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking PDF version of manual ... OK
* DONE

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


Installation output

DAPAR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL DAPAR
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/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 ucrt) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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 
  50.20    2.00   56.18 

Example timings

DAPAR.Rcheck/DAPAR-Ex.timings

nameusersystemelapsed
AggregateMetacell0.480.050.56
BuildAdjacencyMatrix0.270.000.27
BuildColumnToProteinDataset0.330.010.34
BuildMetaCell0.890.050.98
CVDistD_HC2.910.279.68
Children0.010.000.01
CountPep0.300.000.31
ExtendPalette0.030.000.03
GOAnalysisSave000
GetCC3.370.003.38
GetColorsForConditions0.270.000.26
GetDetailedNbPeptides0.310.030.36
GetDetailedNbPeptidesUsed000
GetIndices_BasedOnConditions0.250.000.25
GetIndices_MetacellFiltering0.250.010.27
GetIndices_WholeLine0.360.020.37
GetIndices_WholeMatrix0.370.020.39
GetKeyId0.360.000.36
GetMatAdj0.280.000.28
GetMetacell000
GetMetacellTags0.240.000.24
GetNbPeptidesUsed0.360.010.38
GetNbTags000
GetSoftAvailables000
GetTypeofData0.290.020.30
Get_AllComparisons0.200.010.23
GlobalQuantileAlignment0.30.00.3
GraphPepProt0.310.000.31
LH0000
LH0.lm000
LH1000
LH1.lm000
LOESS1.010.031.05
MeanCentering0.250.000.25
MetaCellFiltering0.380.020.39
MetacellFilteringScope000
Metacell_DIA_NN0.690.000.69
Metacell_generic0.620.000.62
Metacell_maxquant0.630.050.68
Metacell_proline0.710.000.71
NumericalFiltering0.330.000.33
NumericalgetIndicesOfLinesToRemove0.240.000.24
OWAnova0.010.000.01
QuantileCentering0.380.000.38
SetCC2.440.012.45
SetMatAdj0.380.030.40
Set_POV_MEC_tags0.280.030.32
StringBasedFiltering0.470.000.46
StringBasedFiltering20.280.020.30
SumByColumns1.370.021.39
SymFilteringOperators000
UpdateMetacellAfterImputation0.250.010.28
aggregateIter0.520.000.52
aggregateIterParallel000
aggregateMean0.480.020.50
aggregateSum0.440.010.45
aggregateTopn0.370.000.38
applyAnovasOnProteins0.080.000.09
averageIntensities0.520.100.61
barplotEnrichGO_HC 8.31 0.6710.36
barplotGroupGO_HC4.810.345.19
boxPlotD_HC0.250.060.33
buildGraph1.580.001.58
check.conditions0.310.000.31
check.design0.310.000.31
checkClusterability2.310.292.68
classic1wayAnova000
compareNormalizationD_HC0.110.040.17
compute.selection.table0.720.060.90
compute_t_tests0.960.101.05
corrMatrixD_HC0.340.060.42
createMSnset2.580.092.67
createMSnset22.280.052.35
dapar_hc_ExportMenu0.190.170.44
dapar_hc_chart0.080.050.14
deleteLinesFromIndices0.290.000.29
densityPlotD_HC2.240.172.43
diffAnaComputeAdjustedPValues0.110.000.11
diffAnaComputeFDR000
diffAnaGetSignificant0.20.00.2
diffAnaSave0.250.000.25
diffAnaVolcanoplot0.160.020.17
diffAnaVolcanoplot_rCharts0.320.060.41
display.CC.visNet1.490.035.12
enrich_GO4.480.354.85
finalizeAggregation000
findMECBlock0.370.000.38
formatHSDResults000
formatLimmaResult0.130.010.14
formatPHResults000
formatPHTResults000
fudge2LRT000
get.pep.prot.cc1.840.001.84
getDesignLevel0.30.00.3
getIndicesConditions0.170.020.18
getIndicesOfLinesToRemove0.200.010.22
getListNbValuesInLines0.210.000.21
getNumberOf0.340.020.36
getNumberOfEmptyLines0.340.010.36
getPourcentageOfMV0.250.000.25
getProcessingInfo0.250.000.25
getProteinsStats0.290.000.28
getQuantile4Imp0.070.000.07
getTextForAggregation000
getTextForAnaDiff000
getTextForFiltering000
getTextForGOAnalysis000
getTextForHypothesisTest000
getTextForNewDataset000
getTextForNormalization000
getTextForpeptideImputation000
getTextForproteinImputation000
globalAdjPval0.470.020.48
group_GO4.730.224.96
hc_logFC_DensityPlot0.410.080.51
hc_mvTypePlot20.730.060.80
heatmapD0.480.060.54
heatmapForMissingValues0.130.030.16
histPValue_HC0.170.080.26
impute.pa20.410.000.41
inner.aggregate.iter0.400.030.43
inner.aggregate.topn0.350.000.35
inner.mean0.340.010.36
inner.sum0.390.000.39
is.subset000
limmaCompleteTest1.170.001.17
listSheets000
make.contrast0.280.020.30
make.design.10.290.010.29
make.design.20.340.000.35
make.design.30.50.00.5
make.design0.360.000.36
match.metacell0.310.000.31
metacell.def0.020.000.01
metacellHisto_HC0.340.050.41
metacellPerLinesHistoPerCondition_HC0.610.110.75
metacellPerLinesHisto_HC0.700.333.53
metacombine0.050.000.05
mvImage2.530.112.64
my_hc_ExportMenu0.190.152.78
my_hc_chart0.190.214.58
nonzero0.010.010.03
normalizeMethods.dapar000
pepa.test0.250.000.25
pkgs.require000
plotJitter1.660.011.67
plotJitter_rCharts1.400.051.48
plotPCA_Eigen0.440.020.46
plotPCA_Eigen_hc0.330.000.32
plotPCA_Ind0.310.030.35
plotPCA_Var0.330.000.33
postHocTest000
proportionConRev_HC0.060.060.12
rbindMSnset0.410.000.41
reIntroduceMEC0.350.020.36
readExcel000
removeLines0.300.010.31
samLRT000
saveParameters0.210.020.24
scatterplotEnrichGO_HC4.610.184.81
search.metacell.tags000
separateAdjPval0.270.000.27
splitAdjacencyMat0.280.000.28
test.design0.280.020.29
testAnovaModels0.100.020.11
thresholdpval4fdr000
translatedRandomBeta000
univ_AnnotDbPkg0.200.010.22
violinPlotD0.330.030.39
visualizeClusters1.190.071.25
vsn0.720.010.73
wrapper.CVDistD_HC1.340.091.44
wrapper.compareNormalizationD_HC31.63 1.1933.03
wrapper.corrMatrixD_HC0.480.060.56
wrapper.dapar.impute.mi29.78 0.4930.43
wrapper.heatmapD0.580.030.64
wrapper.impute.KNN0.380.020.39
wrapper.impute.detQuant0.390.010.40
wrapper.impute.fixedValue0.420.000.43
wrapper.impute.mle0.360.000.36
wrapper.impute.pa0.120.020.15
wrapper.impute.pa20.390.000.39
wrapper.impute.slsa0.470.010.49
wrapper.mvImage0.160.000.15
wrapper.normalizeD0.280.000.28
wrapper.pca0.120.000.14
wrapperCalibrationPlot0.160.020.21
wrapperClassic1wayAnova000
wrapperRunClustering3.360.013.56
write.excel0.780.041.20
writeMSnsetToCSV0.350.030.53
writeMSnsetToExcel0.750.040.99