Back to Multiple platform build/check report for BioC 3.19:   simplified   long
ABC[D]EFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2024-05-04 11:39:04 -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 lconway


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: /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_1.36.0.tar.gz
StartedAt: 2024-05-03 21:17:06 -0400 (Fri, 03 May 2024)
EndedAt: 2024-05-03 21:28:05 -0400 (Fri, 03 May 2024)
EllapsedTime: 659.5 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_1.36.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/DAPAR.Rcheck’
* using R version 4.4.0 beta (2024-04-14 r86421)
* 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 12.7.1
* 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 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 72.486 42.034 118.166
wrapper.dapar.impute.mi          18.036  1.641  20.098
barplotEnrichGO_HC               10.768  2.598  13.729
checkClusterability               4.803  3.408   8.458
barplotGroupGO_HC                 6.098  0.976   7.222
scatterplotEnrichGO_HC            5.803  0.887   6.844
group_GO                          5.701  0.863   6.699
enrich_GO                         5.527  0.879   6.547
densityPlotD_HC                   3.987  2.233   6.453
* 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-3.19-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 beta (2024-04-14 r86421) -- "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 1.36.0.

  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 
 36.369   1.818  41.574 

Example timings

DAPAR.Rcheck/DAPAR-Ex.timings

nameusersystemelapsed
AggregateMetacell0.4390.0120.454
BuildAdjacencyMatrix1.2540.0201.293
BuildColumnToProteinDataset0.4330.0080.444
BuildMetaCell0.8110.0440.870
CVDistD_HC2.6280.2082.880
Children0.0070.0010.007
CountPep0.3630.0090.374
ExtendPalette0.0350.0050.042
GOAnalysisSave000
GetCC3.2290.0363.291
GetColorsForConditions0.3220.0050.330
GetDetailedNbPeptides0.3350.0060.346
GetDetailedNbPeptidesUsed0.0000.0000.001
GetIndices_BasedOnConditions0.3120.0050.319
GetIndices_MetacellFiltering0.3150.0070.324
GetIndices_WholeLine0.3140.0070.324
GetIndices_WholeMatrix0.3120.0060.321
GetKeyId0.2920.0050.300
GetMatAdj0.3530.0060.360
GetMetacell000
GetMetacellTags0.2960.0050.305
GetNbPeptidesUsed0.3210.0080.333
GetNbTags000
GetSoftAvailables0.0010.0000.001
GetTypeofData0.3260.0060.336
Get_AllComparisons0.2400.0080.252
GlobalQuantileAlignment0.3590.0160.377
GraphPepProt0.3520.0060.361
LH0000
LH0.lm0.0000.0000.001
LH1000
LH1.lm0.0010.0010.000
LOESS0.9720.0221.006
MeanCentering0.3170.0070.328
MetaCellFiltering0.5190.0240.547
MetacellFilteringScope0.0000.0000.001
Metacell_DIA_NN0.5910.0150.611
Metacell_generic0.5000.0150.522
Metacell_maxquant0.5330.0220.562
Metacell_proline0.4760.0120.495
NumericalFiltering0.3420.0080.386
NumericalgetIndicesOfLinesToRemove0.2980.0050.306
OWAnova0.0090.0010.010
QuantileCentering0.2850.0060.294
SetCC2.1190.0362.171
SetMatAdj0.3380.0050.344
Set_POV_MEC_tags0.3070.0050.314
StringBasedFiltering0.3360.0070.346
StringBasedFiltering20.3130.0040.318
SumByColumns1.2770.0291.316
SymFilteringOperators0.0000.0010.001
UpdateMetacellAfterImputation0.3370.0050.345
aggregateIter0.4570.0060.466
aggregateIterParallel0.0000.0010.001
aggregateMean0.4180.0080.428
aggregateSum0.4350.0080.446
aggregateTopn0.3590.0050.366
applyAnovasOnProteins0.0780.0030.081
averageIntensities0.6510.1700.836
barplotEnrichGO_HC10.768 2.59813.729
barplotGroupGO_HC6.0980.9767.222
boxPlotD_HC0.3380.1210.464
buildGraph1.5530.0501.619
check.conditions0.2720.0050.279
check.design0.2940.0060.304
checkClusterability4.8033.4088.458
classic1wayAnova0.0000.0000.001
compareNormalizationD_HC0.1350.0750.214
compute.selection.table0.8240.2151.065
compute_t_tests1.3920.3381.781
corrMatrixD_HC0.4590.0970.562
createMSnset2.0330.1432.220
createMSnset21.9770.1282.130
dapar_hc_ExportMenu0.1760.1810.364
dapar_hc_chart0.0730.0610.139
deleteLinesFromIndices0.3150.0230.341
densityPlotD_HC3.9872.2336.453
diffAnaComputeAdjustedPValues0.1690.0480.223
diffAnaComputeFDR000
diffAnaGetSignificant0.3190.0920.425
diffAnaSave0.2940.0830.386
diffAnaVolcanoplot0.1790.0430.231
diffAnaVolcanoplot_rCharts0.4820.1870.688
display.CC.visNet1.6700.1751.880
enrich_GO5.5270.8796.547
finalizeAggregation0.0000.0010.001
findMECBlock0.3310.0180.353
formatHSDResults0.0000.0000.001
formatLimmaResult0.1610.0370.205
formatPHResults000
formatPHTResults000
fudge2LRT000
get.pep.prot.cc1.5780.0451.636
getDesignLevel0.2740.0050.281
getIndicesConditions0.2900.0030.293
getIndicesOfLinesToRemove0.2910.0120.304
getListNbValuesInLines0.2640.0050.270
getNumberOf0.3050.0180.329
getNumberOfEmptyLines0.2880.0100.301
getPourcentageOfMV0.2820.0160.300
getProcessingInfo0.2860.0050.294
getProteinsStats0.2950.0170.314
getQuantile4Imp0.0650.0030.069
getTextForAggregation0.0000.0010.000
getTextForAnaDiff000
getTextForFiltering000
getTextForGOAnalysis000
getTextForHypothesisTest0.0010.0000.001
getTextForNewDataset0.0030.0010.003
getTextForNormalization0.0010.0000.000
getTextForpeptideImputation0.0000.0010.000
getTextForproteinImputation0.0000.0000.001
globalAdjPval0.4650.0660.541
group_GO5.7010.8636.699
hc_logFC_DensityPlot0.8230.4571.319
hc_mvTypePlot20.9890.4261.459
heatmapD0.6910.0700.768
heatmapForMissingValues0.1690.0300.202
histPValue_HC0.2380.1030.350
impute.pa20.3670.0300.401
inner.aggregate.iter0.3740.0330.417
inner.aggregate.topn0.3420.0200.367
inner.mean0.3130.0150.333
inner.sum0.3680.0220.393
is.subset0.0010.0000.000
limmaCompleteTest1.4970.0941.617
listSheets000
make.contrast0.2900.0050.296
make.design.10.2730.0050.279
make.design.20.3040.0060.313
make.design.30.3030.0060.312
make.design0.2890.0050.297
match.metacell0.5240.0640.595
metacell.def0.0070.0030.009
metacellHisto_HC0.3760.0720.456
metacellPerLinesHistoPerCondition_HC0.5250.1350.667
metacellPerLinesHisto_HC0.6690.3421.072
metacombine0.0820.0100.095
mvImage2.4860.2482.793
my_hc_ExportMenu0.1760.1740.356
my_hc_chart0.1770.1700.354
nonzero0.0270.0020.029
normalizeMethods.dapar0.0000.0010.001
pepa.test0.3520.0190.377
pkgs.require0.0000.0000.001
plotJitter1.6100.0621.689
plotJitter_rCharts1.5880.1351.744
plotPCA_Eigen0.4350.0580.500
plotPCA_Eigen_hc0.2840.0050.293
plotPCA_Ind0.2970.0080.308
plotPCA_Var0.2760.0050.281
postHocTest0.0010.0000.000
proportionConRev_HC0.0610.0650.140
rbindMSnset0.4020.0550.466
reIntroduceMEC0.3570.0330.395
readExcel0.0000.0000.001
removeLines0.3460.0280.378
samLRT000
saveParameters0.2920.0070.301
scatterplotEnrichGO_HC5.8030.8876.844
search.metacell.tags0.0100.0030.014
separateAdjPval0.1730.0200.197
splitAdjacencyMat0.3790.0170.401
test.design0.3440.0050.351
testAnovaModels0.1120.0160.131
thresholdpval4fdr000
translatedRandomBeta0.0020.0060.009
univ_AnnotDbPkg0.2200.0820.309
violinPlotD0.2570.0260.287
visualizeClusters1.6540.3272.030
vsn0.6050.0230.633
wrapper.CVDistD_HC3.0021.6324.790
wrapper.compareNormalizationD_HC 72.486 42.034118.166
wrapper.corrMatrixD_HC0.4330.0940.532
wrapper.dapar.impute.mi18.036 1.64120.098
wrapper.heatmapD0.5550.0460.620
wrapper.impute.KNN0.3630.0260.392
wrapper.impute.detQuant0.4300.0440.482
wrapper.impute.fixedValue0.4100.0460.462
wrapper.impute.mle0.3730.0270.404
wrapper.impute.pa0.2110.0390.254
wrapper.impute.pa20.3770.0340.416
wrapper.impute.slsa0.5790.0940.707
wrapper.mvImage0.1590.0320.195
wrapper.normalizeD0.3580.0080.371
wrapper.pca0.1710.0390.220
wrapperCalibrationPlot0.1990.0430.247
wrapperClassic1wayAnova0.0000.0010.000
wrapperRunClustering2.8520.6283.594
write.excel0.9720.2331.244
writeMSnsetToCSV0.3390.0290.383
writeMSnsetToExcel1.1850.3561.604