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This page was generated on 2024-05-04 11:36:27 -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 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: 1.36.0
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_1.36.0.tar.gz
StartedAt: 2024-05-03 22:23:01 -0400 (Fri, 03 May 2024)
EndedAt: 2024-05-03 22:30:49 -0400 (Fri, 03 May 2024)
EllapsedTime: 467.9 seconds
RetCode: 0
Status:   OK  
CheckDir: DAPAR.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### 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_1.36.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/DAPAR.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* 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 ‘1.36.0’
* 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 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 34.144  9.449  44.201
wrapper.dapar.impute.mi          13.452  0.267  13.736
barplotEnrichGO_HC                8.147  0.745   9.044
barplotGroupGO_HC                 4.817  0.232   5.061
* 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 beta (2024-04-15 r86425) -- "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 1.36.0.

  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 
 29.732   1.353  31.122 

Example timings

DAPAR.Rcheck/DAPAR-Ex.timings

nameusersystemelapsed
AggregateMetacell0.3600.0120.373
BuildAdjacencyMatrix1.0670.1441.210
BuildColumnToProteinDataset0.3420.0040.346
BuildMetaCell0.6360.0360.674
CVDistD_HC1.8930.0771.988
Children0.0040.0000.005
CountPep0.2880.0160.305
ExtendPalette0.0260.0040.031
GOAnalysisSave000
GetCC3.0700.0003.069
GetColorsForConditions0.2410.0030.245
GetDetailedNbPeptides0.2630.0040.267
GetDetailedNbPeptidesUsed000
GetIndices_BasedOnConditions0.2600.0040.264
GetIndices_MetacellFiltering0.2680.0040.273
GetIndices_WholeLine0.2660.0080.275
GetIndices_WholeMatrix0.2580.0040.262
GetKeyId0.2410.0040.245
GetMatAdj0.2840.0080.292
GetMetacell000
GetMetacellTags0.270.000.27
GetNbPeptidesUsed0.2650.0040.269
GetNbTags000
GetSoftAvailables0.0010.0000.000
GetTypeofData0.2490.0030.253
Get_AllComparisons0.2010.0090.210
GlobalQuantileAlignment0.3110.0030.314
GraphPepProt0.2680.0000.267
LH0000
LH0.lm000
LH1000
LH1.lm0.0010.0000.000
LOESS0.9500.0040.956
MeanCentering0.2590.0080.267
MetaCellFiltering0.4250.0080.433
MetacellFilteringScope000
Metacell_DIA_NN0.490.020.51
Metacell_generic0.3930.0080.401
Metacell_maxquant0.4380.0040.442
Metacell_proline0.4060.0110.417
NumericalFiltering0.2820.0040.286
NumericalgetIndicesOfLinesToRemove0.2550.0000.255
OWAnova0.0080.0000.008
QuantileCentering0.2450.0000.245
SetCC2.0750.1402.215
SetMatAdj0.2800.0040.284
Set_POV_MEC_tags0.2470.0080.255
StringBasedFiltering0.2850.0040.288
StringBasedFiltering20.2780.0000.278
SumByColumns1.0340.0481.081
SymFilteringOperators000
UpdateMetacellAfterImputation0.2770.0000.277
aggregateIter0.3970.0120.408
aggregateIterParallel000
aggregateMean0.3640.0040.367
aggregateSum0.3520.0000.352
aggregateTopn0.3090.0040.313
applyAnovasOnProteins0.0760.0040.080
averageIntensities0.4410.0410.531
barplotEnrichGO_HC8.1470.7459.044
barplotGroupGO_HC4.8170.2325.061
boxPlotD_HC0.2840.0320.321
buildGraph1.8540.0881.942
check.conditions0.2560.0000.256
check.design0.2480.0040.251
checkClusterability2.4860.7863.330
classic1wayAnova000
compareNormalizationD_HC0.1170.0040.123
compute.selection.table0.6490.0390.692
compute_t_tests0.9650.0761.045
corrMatrixD_HC0.4360.1831.246
createMSnset1.6560.8192.546
createMSnset21.5620.0321.594
dapar_hc_ExportMenu0.1090.0360.147
dapar_hc_chart0.0460.0120.058
deleteLinesFromIndices0.2790.0080.287
densityPlotD_HC2.1470.5422.721
diffAnaComputeAdjustedPValues0.1270.0160.143
diffAnaComputeFDR0.0000.0010.000
diffAnaGetSignificant0.1970.0360.233
diffAnaSave0.2030.0110.215
diffAnaVolcanoplot0.1250.0160.142
diffAnaVolcanoplot_rCharts0.3380.0480.387
display.CC.visNet1.5060.0721.584
enrich_GO4.500.204.74
finalizeAggregation0.0000.0000.001
findMECBlock0.2800.0120.293
formatHSDResults000
formatLimmaResult0.1150.0080.124
formatPHResults0.0000.0000.001
formatPHTResults000
fudge2LRT000
get.pep.prot.cc1.6360.0231.659
getDesignLevel0.2430.0000.242
getIndicesConditions0.2390.0000.239
getIndicesOfLinesToRemove0.250.000.25
getListNbValuesInLines0.2220.0120.234
getNumberOf0.2500.0080.257
getNumberOfEmptyLines0.2540.0080.262
getPourcentageOfMV0.2530.0080.261
getProcessingInfo0.250.000.25
getProteinsStats0.2530.0080.261
getQuantile4Imp0.0580.0000.058
getTextForAggregation000
getTextForAnaDiff0.0010.0000.000
getTextForFiltering000
getTextForGOAnalysis0.0010.0000.000
getTextForHypothesisTest0.0010.0000.000
getTextForNewDataset0.0020.0000.002
getTextForNormalization000
getTextForpeptideImputation0.0010.0000.000
getTextForproteinImputation0.0010.0000.000
globalAdjPval0.3310.0150.348
group_GO4.4370.2214.669
hc_logFC_DensityPlot0.4440.0740.525
hc_mvTypePlot20.6220.0900.720
heatmapD0.5980.0320.637
heatmapForMissingValues0.1450.0040.150
histPValue_HC0.1750.0120.187
impute.pa20.2970.0110.309
inner.aggregate.iter0.3030.0000.303
inner.aggregate.topn0.2790.0040.283
inner.mean0.2800.0030.284
inner.sum0.3290.0050.334
is.subset0.0000.0010.001
limmaCompleteTest1.0960.0181.118
listSheets000
make.contrast0.2590.0120.271
make.design.10.2750.0020.278
make.design.20.2750.0000.274
make.design.30.2810.0000.283
make.design0.2810.0000.281
match.metacell0.5460.0370.709
metacell.def0.0010.0040.005
metacellHisto_HC0.3130.0240.347
metacellPerLinesHistoPerCondition_HC0.4400.0130.453
metacellPerLinesHisto_HC0.5110.0440.556
metacombine0.0530.0000.054
mvImage1.7940.0281.826
my_hc_ExportMenu0.1090.0280.138
my_hc_chart0.1110.0330.144
nonzero0.0210.0000.021
normalizeMethods.dapar0.0010.0000.000
pepa.test0.2830.0030.286
pkgs.require000
plotJitter1.6390.0071.646
plotJitter_rCharts1.3650.0601.426
plotPCA_Eigen0.3000.0160.322
plotPCA_Eigen_hc0.2360.0000.235
plotPCA_Ind0.2420.0030.247
plotPCA_Var0.2320.0040.236
postHocTest0.0000.0010.001
proportionConRev_HC0.0280.0190.047
rbindMSnset0.3060.0160.323
reIntroduceMEC0.2890.0050.293
readExcel0.0010.0000.000
removeLines0.2680.0080.276
samLRT0.0000.0000.001
saveParameters0.2380.0030.241
scatterplotEnrichGO_HC4.4850.1564.651
search.metacell.tags0.0020.0040.006
separateAdjPval0.1290.0200.149
splitAdjacencyMat0.2890.0000.290
test.design0.2670.0040.272
testAnovaModels0.0810.0040.085
thresholdpval4fdr0.0000.0000.001
translatedRandomBeta0.0050.0040.009
univ_AnnotDbPkg0.1230.0490.172
violinPlotD0.3680.0150.387
visualizeClusters1.0270.0661.095
vsn0.4880.0040.493
wrapper.CVDistD_HC1.3880.2951.702
wrapper.compareNormalizationD_HC34.144 9.44944.201
wrapper.corrMatrixD_HC0.3120.0240.335
wrapper.dapar.impute.mi13.452 0.26713.736
wrapper.heatmapD0.4670.0230.490
wrapper.impute.KNN0.2920.0120.304
wrapper.impute.detQuant0.2940.0040.299
wrapper.impute.fixedValue0.2960.0110.309
wrapper.impute.mle0.2690.0000.268
wrapper.impute.pa0.0720.0230.097
wrapper.impute.pa20.2610.0120.274
wrapper.impute.slsa0.3790.0000.380
wrapper.mvImage0.1080.0070.115
wrapper.normalizeD0.2440.0040.247
wrapper.pca0.1080.0040.112
wrapperCalibrationPlot0.1450.0120.157
wrapperClassic1wayAnova000
wrapperRunClustering1.6870.1621.854
write.excel0.5670.0650.637
writeMSnsetToCSV0.2570.0030.262
writeMSnsetToExcel0.7140.0660.784