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This page was generated on 2024-05-04 11:40:26 -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 kunpeng2


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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: DAPAR
Version: 1.36.0
Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:DAPAR.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings DAPAR_1.36.0.tar.gz
StartedAt: 2024-05-04 06:37:22 -0000 (Sat, 04 May 2024)
EndedAt: 2024-05-04 06:47:38 -0000 (Sat, 04 May 2024)
EllapsedTime: 616.0 seconds
RetCode: 0
Status:   OK  
CheckDir: DAPAR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:DAPAR.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --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: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* 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 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 56.593 12.763  66.619
wrapper.dapar.impute.mi          20.826  0.445  21.176
barplotEnrichGO_HC               10.185  1.074  11.037
barplotGroupGO_HC                 6.069  0.274   6.333
scatterplotEnrichGO_HC            5.672  0.254   5.890
group_GO                          5.529  0.272   5.746
enrich_GO                         5.507  0.290   5.762
checkClusterability               3.926  1.121   4.835
* 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/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL DAPAR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/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: aarch64-unknown-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 
 41.733   0.950  42.848 

Example timings

DAPAR.Rcheck/DAPAR-Ex.timings

nameusersystemelapsed
AggregateMetacell0.4320.0120.447
BuildAdjacencyMatrix1.2580.1231.384
BuildColumnToProteinDataset0.4110.0080.419
BuildMetaCell0.7180.0240.746
CVDistD_HC3.1570.2863.512
Children0.0020.0030.006
CountPep0.3290.0200.350
ExtendPalette0.0360.0000.037
GOAnalysisSave000
GetCC3.5970.1953.806
GetColorsForConditions0.2870.0000.287
GetDetailedNbPeptides0.3080.0110.321
GetDetailedNbPeptidesUsed000
GetIndices_BasedOnConditions0.2980.0160.314
GetIndices_MetacellFiltering0.3060.0080.314
GetIndices_WholeLine0.3050.0000.306
GetIndices_WholeMatrix0.3070.0040.313
GetKeyId0.2790.0080.288
GetMatAdj0.3520.0080.360
GetMetacell000
GetMetacellTags0.3000.0080.308
GetNbPeptidesUsed0.3040.0160.321
GetNbTags000
GetSoftAvailables0.0010.0000.001
GetTypeofData0.2810.0080.289
Get_AllComparisons0.2860.0040.292
GlobalQuantileAlignment0.3460.0040.350
GraphPepProt0.3120.0080.321
LH0000
LH0.lm000
LH1000
LH1.lm000
LOESS1.6960.0081.708
MeanCentering0.2890.0200.309
MetaCellFiltering0.5390.0280.569
MetacellFilteringScope000
Metacell_DIA_NN0.5560.0160.574
Metacell_generic0.4860.0040.492
Metacell_maxquant0.5310.0040.537
Metacell_proline0.4810.0040.486
NumericalFiltering0.3350.0000.335
NumericalgetIndicesOfLinesToRemove0.2920.0040.297
OWAnova0.0080.0000.008
QuantileCentering0.2730.0040.279
SetCC2.3840.1322.522
SetMatAdj0.3440.0080.352
Set_POV_MEC_tags0.2960.0040.300
StringBasedFiltering0.3380.0000.338
StringBasedFiltering20.3250.0080.333
SumByColumns1.6120.0591.679
SymFilteringOperators000
UpdateMetacellAfterImputation0.3030.0040.308
aggregateIter0.4860.0000.487
aggregateIterParallel000
aggregateMean0.4280.0160.445
aggregateSum0.4140.0000.415
aggregateTopn0.3670.0000.368
applyAnovasOnProteins0.0870.0000.087
averageIntensities0.5360.0410.567
barplotEnrichGO_HC10.185 1.07411.037
barplotGroupGO_HC6.0690.2746.333
boxPlotD_HC0.3780.0610.427
buildGraph1.7230.0641.784
check.conditions0.2720.0000.273
check.design0.2790.0000.280
checkClusterability3.9261.1214.835
classic1wayAnova000
compareNormalizationD_HC0.1320.0120.145
compute.selection.table0.8160.0600.878
compute_t_tests1.3640.0831.449
corrMatrixD_HC0.5040.0240.529
createMSnset1.9920.0672.063
createMSnset21.9180.0561.977
dapar_hc_ExportMenu0.1590.0280.189
dapar_hc_chart0.0700.0080.078
deleteLinesFromIndices0.3250.0080.333
densityPlotD_HC3.3810.8214.021
diffAnaComputeAdjustedPValues0.1700.0070.178
diffAnaComputeFDR000
diffAnaGetSignificant0.2700.0360.307
diffAnaSave0.2650.0160.282
diffAnaVolcanoplot0.1480.0210.164
diffAnaVolcanoplot_rCharts0.4580.0610.499
display.CC.visNet1.8140.1361.949
enrich_GO5.5070.2905.762
finalizeAggregation000
findMECBlock0.3140.0120.324
formatHSDResults000
formatLimmaResult0.1530.0080.156
formatPHResults000
formatPHTResults000
fudge2LRT000
get.pep.prot.cc1.6710.0081.680
getDesignLevel0.2650.0030.269
getIndicesConditions0.2620.0070.271
getIndicesOfLinesToRemove0.2880.0080.295
getListNbValuesInLines0.2690.0000.269
getNumberOf0.2890.0150.303
getNumberOfEmptyLines0.3150.0000.315
getPourcentageOfMV0.2950.0040.297
getProcessingInfo0.2670.0000.267
getProteinsStats0.2970.0120.307
getQuantile4Imp0.0610.0000.060
getTextForAggregation0.0000.0000.001
getTextForAnaDiff0.0000.0000.001
getTextForFiltering000
getTextForGOAnalysis000
getTextForHypothesisTest000
getTextForNewDataset0.0020.0000.003
getTextForNormalization0.0000.0000.001
getTextForpeptideImputation000
getTextForproteinImputation0.0010.0000.000
globalAdjPval0.4960.0370.523
group_GO5.5290.2725.746
hc_logFC_DensityPlot0.6700.2010.821
hc_mvTypePlot20.8170.1080.927
heatmapD0.6810.0200.701
heatmapForMissingValues0.1540.0120.167
histPValue_HC0.2120.0290.236
impute.pa20.3500.0120.358
inner.aggregate.iter0.3550.0160.368
inner.aggregate.topn0.3170.0160.331
inner.mean0.3280.0040.330
inner.sum0.3970.0000.395
is.subset0.0010.0000.000
limmaCompleteTest1.7230.0641.784
listSheets000
make.contrast0.2940.0000.295
make.design.10.2930.0000.294
make.design.20.2990.0000.299
make.design.30.2960.0030.299
make.design0.2990.0040.303
match.metacell0.5410.0160.558
metacell.def0.0060.0000.006
metacellHisto_HC0.3620.0080.370
metacellPerLinesHistoPerCondition_HC0.5000.0560.552
metacellPerLinesHisto_HC0.6210.0890.704
metacombine0.0870.0040.089
mvImage2.7460.1042.843
my_hc_ExportMenu0.1550.0400.194
my_hc_chart0.1610.0320.190
nonzero0.0230.0000.023
normalizeMethods.dapar000
pepa.test0.3230.0000.323
pkgs.require000
plotJitter1.7660.0711.843
plotJitter_rCharts1.6580.0231.681
plotPCA_Eigen0.3610.0070.369
plotPCA_Eigen_hc0.2690.0040.272
plotPCA_Ind0.2770.0040.281
plotPCA_Var0.2760.0040.281
postHocTest000
proportionConRev_HC0.0590.0160.072
rbindMSnset0.4000.0200.414
reIntroduceMEC0.3430.0170.356
readExcel000
removeLines0.3220.0160.335
samLRT000
saveParameters0.2780.0000.278
scatterplotEnrichGO_HC5.6720.2545.890
search.metacell.tags0.0110.0000.011
separateAdjPval0.1730.0130.182
splitAdjacencyMat0.3300.0030.333
test.design0.2980.0000.299
testAnovaModels0.1000.0050.102
thresholdpval4fdr000
translatedRandomBeta0.0020.0000.003
univ_AnnotDbPkg0.2050.0200.222
violinPlotD0.4420.0120.451
visualizeClusters1.6770.1691.774
vsn0.6410.0120.651
wrapper.CVDistD_HC2.2810.4992.668
wrapper.compareNormalizationD_HC56.59312.76366.619
wrapper.corrMatrixD_HC0.4340.0280.457
wrapper.dapar.impute.mi20.826 0.44521.176
wrapper.heatmapD0.5630.0160.576
wrapper.impute.KNN0.3290.0030.330
wrapper.impute.detQuant0.3520.0290.377
wrapper.impute.fixedValue0.3720.0200.385
wrapper.impute.mle0.3190.0110.328
wrapper.impute.pa0.1160.0080.121
wrapper.impute.pa20.3340.0080.338
wrapper.impute.slsa0.5050.0330.529
wrapper.mvImage0.1470.0160.158
wrapper.normalizeD0.2980.0040.302
wrapper.pca0.1440.0120.152
wrapperCalibrationPlot0.1720.0290.195
wrapperClassic1wayAnova000
wrapperRunClustering2.6650.2252.866
write.excel0.7690.1160.855
writeMSnsetToCSV0.2900.0200.312
writeMSnsetToExcel1.0690.1171.165