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This page was generated on 2024-05-04 11:37:39 -0400 (Sat, 04 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4519
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4479
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 1.36.0  (landing page)
Samuel Wieczorek
Snapshot Date: 2024-05-03 14:00:19 -0400 (Fri, 03 May 2024)
git_url: https://git.bioconductor.org/packages/DAPAR
git_branch: RELEASE_3_19
git_last_commit: 1235415
git_last_commit_date: 2024-04-30 10:45:58 -0400 (Tue, 30 Apr 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
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for DAPAR on palomino3


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: 1.36.0
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:DAPAR.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings DAPAR_1.36.0.tar.gz
StartedAt: 2024-05-04 02:25:30 -0400 (Sat, 04 May 2024)
EndedAt: 2024-05-04 02:34:46 -0400 (Sat, 04 May 2024)
EllapsedTime: 556.1 seconds
RetCode: 0
Status:   OK  
CheckDir: DAPAR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:DAPAR.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings DAPAR_1.36.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/DAPAR.Rcheck'
* using R version 4.4.0 beta (2024-04-15 r86425 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* 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 '1.36.0'
* 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 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 30.27   1.25   32.17
wrapper.dapar.impute.mi          28.77   0.50   29.31
barplotEnrichGO_HC                8.46   1.10   18.84
barplotGroupGO_HC                 5.39   0.53    6.25
scatterplotEnrichGO_HC            4.91   0.45    5.36
group_GO                          4.72   0.30    5.03
CVDistD_HC                        2.59   0.36    6.47
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking PDF version of manual ... OK
* DONE

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


Installation output

DAPAR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL DAPAR
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-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 4.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup"
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 1.36.0.

  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 
  49.25    2.10   52.04 

Example timings

DAPAR.Rcheck/DAPAR-Ex.timings

nameusersystemelapsed
AggregateMetacell0.310.030.36
BuildAdjacencyMatrix1.090.001.09
BuildColumnToProteinDataset0.280.000.29
BuildMetaCell0.700.000.73
CVDistD_HC2.590.366.47
Children000
CountPep0.410.020.42
ExtendPalette0.050.000.05
GOAnalysisSave000
GetCC3.390.013.41
GetColorsForConditions0.260.040.29
GetDetailedNbPeptides0.380.000.38
GetDetailedNbPeptidesUsed000
GetIndices_BasedOnConditions0.340.000.34
GetIndices_MetacellFiltering0.360.000.36
GetIndices_WholeLine0.310.000.31
GetIndices_WholeMatrix0.360.000.36
GetKeyId0.350.000.35
GetMatAdj0.310.010.33
GetMetacell000
GetMetacellTags0.250.030.28
GetNbPeptidesUsed0.260.020.28
GetNbTags000
GetSoftAvailables000
GetTypeofData0.240.000.23
Get_AllComparisons0.230.000.25
GlobalQuantileAlignment0.440.000.44
GraphPepProt0.380.000.37
LH0000
LH0.lm000
LH1000
LH1.lm000
LOESS0.870.020.89
MeanCentering0.30.00.3
MetaCellFiltering0.450.000.45
MetacellFilteringScope000
Metacell_DIA_NN0.70.00.7
Metacell_generic0.520.050.56
Metacell_maxquant0.580.010.59
Metacell_proline0.410.000.42
NumericalFiltering0.230.020.25
NumericalgetIndicesOfLinesToRemove0.220.000.22
OWAnova0.010.000.02
QuantileCentering0.190.030.22
SetCC2.220.012.22
SetMatAdj0.410.000.40
Set_POV_MEC_tags0.310.000.31
StringBasedFiltering0.260.000.27
StringBasedFiltering20.250.020.26
SumByColumns1.040.091.13
SymFilteringOperators000
UpdateMetacellAfterImputation0.250.000.26
aggregateIter0.390.000.39
aggregateIterParallel000
aggregateMean0.310.020.33
aggregateSum0.410.010.42
aggregateTopn0.420.000.42
applyAnovasOnProteins0.060.000.07
averageIntensities0.470.090.57
barplotEnrichGO_HC 8.46 1.1018.84
barplotGroupGO_HC5.390.536.25
boxPlotD_HC0.290.120.66
buildGraph1.600.001.59
check.conditions0.200.000.21
check.design0.270.020.28
checkClusterability2.200.222.45
classic1wayAnova000
compareNormalizationD_HC0.130.160.47
compute.selection.table0.680.060.78
compute_t_tests1.030.061.10
corrMatrixD_HC0.380.090.65
createMSnset2.010.052.08
createMSnset22.290.112.39
dapar_hc_ExportMenu0.250.221.23
dapar_hc_chart0.090.080.43
deleteLinesFromIndices0.230.010.25
densityPlotD_HC2.100.222.81
diffAnaComputeAdjustedPValues0.140.020.16
diffAnaComputeFDR000
diffAnaGetSignificant0.230.000.23
diffAnaSave0.160.000.16
diffAnaVolcanoplot0.090.030.12
diffAnaVolcanoplot_rCharts0.360.110.75
display.CC.visNet1.670.042.22
enrich_GO4.520.384.89
finalizeAggregation000
findMECBlock0.320.000.33
formatHSDResults000
formatLimmaResult0.140.000.14
formatPHResults000
formatPHTResults000
fudge2LRT000
get.pep.prot.cc1.570.001.56
getDesignLevel0.220.000.22
getIndicesConditions0.310.000.31
getIndicesOfLinesToRemove0.250.020.27
getListNbValuesInLines0.220.000.21
getNumberOf0.280.000.29
getNumberOfEmptyLines0.250.000.25
getPourcentageOfMV0.200.010.21
getProcessingInfo0.240.000.24
getProteinsStats0.290.000.30
getQuantile4Imp0.080.020.09
getTextForAggregation000
getTextForAnaDiff000
getTextForFiltering000
getTextForGOAnalysis000
getTextForHypothesisTest000
getTextForNewDataset000
getTextForNormalization000
getTextForpeptideImputation0.020.000.01
getTextForproteinImputation000
globalAdjPval0.430.010.46
group_GO4.720.305.03
hc_logFC_DensityPlot0.470.110.86
hc_mvTypePlot20.730.061.05
heatmapD0.720.030.77
heatmapForMissingValues0.170.000.17
histPValue_HC0.220.110.58
impute.pa20.340.020.36
inner.aggregate.iter0.410.000.40
inner.aggregate.topn0.390.000.39
inner.mean0.330.000.33
inner.sum0.300.010.31
is.subset000
limmaCompleteTest1.300.041.33
listSheets000
make.contrast0.250.000.25
make.design.10.260.000.26
make.design.20.240.010.25
make.design.30.360.000.36
make.design0.340.020.36
match.metacell0.380.000.38
metacell.def0.010.000.01
metacellHisto_HC0.440.090.81
metacellPerLinesHistoPerCondition_HC0.560.271.32
metacellPerLinesHisto_HC0.640.502.84
metacombine0.080.000.09
mvImage2.090.072.16
my_hc_ExportMenu0.220.241.27
my_hc_chart0.250.221.14
nonzero0.030.000.03
normalizeMethods.dapar000
pepa.test0.220.060.28
pkgs.require000
plotJitter1.610.021.62
plotJitter_rCharts1.600.091.97
plotPCA_Eigen0.390.050.44
plotPCA_Eigen_hc0.250.000.25
plotPCA_Ind0.280.000.28
plotPCA_Var0.330.010.35
postHocTest000
proportionConRev_HC0.070.080.42
rbindMSnset0.350.000.34
reIntroduceMEC0.280.020.30
readExcel000
removeLines0.220.030.25
samLRT000
saveParameters0.230.000.23
scatterplotEnrichGO_HC4.910.455.36
search.metacell.tags000
separateAdjPval0.250.000.25
splitAdjacencyMat0.390.000.39
test.design0.330.020.35
testAnovaModels0.080.000.09
thresholdpval4fdr000
translatedRandomBeta0.000.010.02
univ_AnnotDbPkg0.180.060.25
violinPlotD0.290.020.31
visualizeClusters1.070.031.11
vsn0.880.020.89
wrapper.CVDistD_HC1.170.181.56
wrapper.compareNormalizationD_HC30.27 1.2532.17
wrapper.corrMatrixD_HC0.370.081.38
wrapper.dapar.impute.mi28.77 0.5029.31
wrapper.heatmapD0.530.080.61
wrapper.impute.KNN0.360.020.38
wrapper.impute.detQuant0.360.000.36
wrapper.impute.fixedValue0.260.010.28
wrapper.impute.mle0.320.030.32
wrapper.impute.pa0.100.000.11
wrapper.impute.pa20.30.00.3
wrapper.impute.slsa0.490.030.52
wrapper.mvImage0.120.000.12
wrapper.normalizeD0.250.030.28
wrapper.pca0.140.000.14
wrapperCalibrationPlot0.130.020.14
wrapperClassic1wayAnova000
wrapperRunClustering1.970.122.11
write.excel0.620.060.83
writeMSnsetToCSV0.230.020.39
writeMSnsetToExcel0.960.011.14