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This page was generated on 2024-11-20 12:07 -0500 (Wed, 20 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4481
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4479
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4359
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4539
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
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: 2024-11-19 13:40 -0500 (Tue, 19 Nov 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)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  
palomino8Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
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  


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: 1.38.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:DAPAR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings DAPAR_1.38.0.tar.gz
StartedAt: 2024-11-20 06:54:02 -0000 (Wed, 20 Nov 2024)
EndedAt: 2024-11-20 07:04:44 -0000 (Wed, 20 Nov 2024)
EllapsedTime: 642.0 seconds
RetCode: 0
Status:   OK  
CheckDir: DAPAR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:DAPAR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings DAPAR_1.38.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/DAPAR.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
    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 ‘1.38.0’
* 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 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 60.329 16.967  72.907
wrapper.dapar.impute.mi          22.491  0.499  22.976
barplotEnrichGO_HC                9.989  1.014  10.963
barplotGroupGO_HC                 5.698  0.385   6.010
scatterplotEnrichGO_HC            5.350  0.276   5.608
group_GO                          5.319  0.295   5.545
enrich_GO                         5.274  0.281   5.533
checkClusterability               4.196  1.200   4.955
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking PDF version of manual ... OK
* DONE

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


Installation output

DAPAR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL DAPAR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.4.1/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 4.4.1 (2024-06-14) -- "Race for Your Life"
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 1.38.0.

  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 
 41.317   1.733  43.293 

Example timings

DAPAR.Rcheck/DAPAR-Ex.timings

nameusersystemelapsed
AggregateMetacell0.4050.0120.420
BuildAdjacencyMatrix0.3100.0080.318
BuildColumnToProteinDataset0.3970.0080.407
BuildMetaCell0.6930.0280.725
CVDistD_HC3.2320.0483.334
Children0.0030.0040.006
CountPep1.3690.0641.434
ExtendPalette0.0350.0000.035
GOAnalysisSave000
GetCC2.6940.0442.742
GetColorsForConditions0.2560.0080.264
GetDetailedNbPeptides0.2970.0000.297
GetDetailedNbPeptidesUsed000
GetIndices_BasedOnConditions0.2850.0040.289
GetIndices_MetacellFiltering0.2910.0040.296
GetIndices_WholeLine0.2840.0040.289
GetIndices_WholeMatrix0.2830.0080.291
GetKeyId0.2630.0040.267
GetMatAdj0.3390.0080.347
GetMetacell0.0010.0000.000
GetMetacellTags0.2820.0080.290
GetNbPeptidesUsed0.2870.0080.296
GetNbTags000
GetSoftAvailables0.0000.0010.001
GetTypeofData0.2530.0190.272
Get_AllComparisons0.2880.0080.297
GlobalQuantileAlignment0.2980.0040.303
GraphPepProt0.3030.0000.304
LH0000
LH0.lm000
LH1000
LH1.lm000
LOESS1.7060.0001.708
MeanCentering0.3150.0080.322
MetaCellFiltering0.5220.0000.523
MetacellFilteringScope000
Metacell_DIA_NN0.5860.0160.603
Metacell_generic0.4950.0080.505
Metacell_maxquant0.5610.0000.563
Metacell_proline0.5090.0040.514
NumericalFiltering0.3320.0040.336
NumericalgetIndicesOfLinesToRemove0.2830.0000.284
OWAnova0.0040.0030.008
QuantileCentering0.2720.0000.273
SetCC2.6110.0672.684
SetMatAdj0.3250.0080.333
Set_POV_MEC_tags0.2860.0040.290
StringBasedFiltering0.3340.0040.339
StringBasedFiltering20.3260.0000.328
SumByColumns1.6480.0001.652
SymFilteringOperators000
UpdateMetacellAfterImputation0.3020.0040.307
aggregateIter0.5230.0080.532
aggregateIterParallel0.0010.0000.000
aggregateMean0.3960.0080.404
aggregateSum0.4250.0080.434
aggregateTopn0.3850.0040.390
applyAnovasOnProteins0.0920.0000.092
averageIntensities0.4970.1000.587
barplotEnrichGO_HC 9.989 1.01410.963
barplotGroupGO_HC5.6980.3856.010
boxPlotD_HC0.3530.0330.374
buildGraph1.7810.0881.874
check.conditions0.2520.0040.256
check.design0.2580.0000.258
checkClusterability4.1961.2004.955
classic1wayAnova000
compareNormalizationD_HC0.1260.0240.148
compute.selection.table0.8620.0830.919
compute_t_tests1.4060.1901.528
corrMatrixD_HC0.5000.0240.519
createMSnset2.0170.1082.111
createMSnset22.0190.0522.058
dapar_hc_ExportMenu0.1690.0310.195
dapar_hc_chart0.0800.0040.082
deleteLinesFromIndices0.2980.0240.318
densityPlotD_HC3.4870.8423.992
diffAnaComputeAdjustedPValues0.1450.0290.167
diffAnaComputeFDR000
diffAnaGetSignificant0.2880.0200.294
diffAnaSave0.2590.0370.283
diffAnaVolcanoplot0.1430.0290.166
diffAnaVolcanoplot_rCharts0.4070.0660.452
display.CC.visNet1.8510.0791.920
enrich_GO5.2740.2815.533
finalizeAggregation000
findMECBlock0.3040.0000.302
formatHSDResults000
formatLimmaResult0.1330.0200.149
formatPHResults000
formatPHTResults000
fudge2LRT000
get.pep.prot.cc1.7630.0071.769
getDesignLevel0.2480.0000.248
getIndicesConditions0.2420.0060.248
getIndicesOfLinesToRemove0.2740.0030.276
getListNbValuesInLines0.2480.0000.249
getNumberOf0.2600.0160.275
getNumberOfEmptyLines0.2970.0040.300
getPourcentageOfMV0.2790.0040.281
getProcessingInfo0.2480.0000.247
getProteinsStats0.2910.0030.293
getQuantile4Imp0.0620.0000.061
getTextForAggregation0.0010.0000.001
getTextForAnaDiff0.0000.0000.001
getTextForFiltering000
getTextForGOAnalysis000
getTextForHypothesisTest000
getTextForNewDataset0.0030.0000.003
getTextForNormalization0.0010.0000.001
getTextForpeptideImputation000
getTextForproteinImputation000
globalAdjPval0.5220.0210.531
group_GO5.3190.2955.545
hc_logFC_DensityPlot0.7290.1410.804
hc_mvTypePlot21.0450.0971.080
heatmapD0.5950.0280.621
heatmapForMissingValues0.1650.0120.173
histPValue_HC0.2180.0290.239
impute.pa20.3420.0040.341
inner.aggregate.iter0.3380.0160.350
inner.aggregate.topn0.3050.0080.310
inner.mean0.3680.0000.367
inner.sum0.3000.0090.307
is.subset0.0000.0010.001
limmaCompleteTest1.7770.0541.815
listSheets000
make.contrast0.2780.0000.278
make.design.10.2760.0000.276
make.design.20.2740.0030.278
make.design.30.4470.0000.448
make.design0.2730.0000.273
match.metacell0.2960.0150.311
metacell.def0.0060.0000.006
metacellHisto_HC0.3440.0080.353
metacellPerLinesHistoPerCondition_HC0.4850.0200.506
metacellPerLinesHisto_HC0.6430.0650.853
metacombine0.0830.0080.090
mvImage2.7840.1582.908
my_hc_ExportMenu0.1610.0330.196
my_hc_chart0.1640.0270.193
nonzero0.0230.0000.023
normalizeMethods.dapar000
pepa.test0.3040.0040.308
pkgs.require000
plotJitter1.8280.0591.890
plotJitter_rCharts1.6800.0421.726
plotPCA_Eigen0.3500.0040.355
plotPCA_Eigen_hc0.2560.0000.256
plotPCA_Ind0.2710.0030.275
plotPCA_Var0.2600.0000.261
postHocTest000
proportionConRev_HC0.0550.0120.067
rbindMSnset0.3730.0120.385
reIntroduceMEC0.3080.0240.333
readExcel000
removeLines0.3150.0040.316
samLRT000
saveParameters0.2590.0000.259
scatterplotEnrichGO_HC5.3500.2765.608
search.metacell.tags0.0090.0010.009
separateAdjPval0.1670.0110.179
splitAdjacencyMat0.3000.0110.313
test.design0.2810.0030.284
testAnovaModels0.0990.0090.105
thresholdpval4fdr000
translatedRandomBeta0.0030.0000.003
univ_AnnotDbPkg0.2130.0000.213
violinPlotD0.4450.0190.469
visualizeClusters1.6190.1501.697
vsn0.6670.0120.675
wrapper.CVDistD_HC2.2400.6172.734
wrapper.compareNormalizationD_HC60.32916.96772.907
wrapper.corrMatrixD_HC0.5520.0140.569
wrapper.dapar.impute.mi22.491 0.49922.976
wrapper.heatmapD0.5000.0150.514
wrapper.impute.KNN0.3040.0200.320
wrapper.impute.detQuant0.3530.0360.384
wrapper.impute.fixedValue0.3470.0530.392
wrapper.impute.mle0.3130.0160.325
wrapper.impute.pa0.1230.0120.130
wrapper.impute.pa20.3080.0240.328
wrapper.impute.slsa0.4990.0530.541
wrapper.mvImage0.1470.0290.170
wrapper.normalizeD0.3610.0190.381
wrapper.pca0.1310.0340.163
wrapperCalibrationPlot0.1720.0350.201
wrapperClassic1wayAnova0.0000.0000.001
wrapperRunClustering2.7450.4683.161
write.excel0.7250.1240.830
writeMSnsetToCSV0.2930.0030.299
writeMSnsetToExcel0.9790.1621.124