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This page was generated on 2022-10-19 13:22:48 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
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

CHECK results for DAPAR on merida1


To the developers/maintainers of the DAPAR package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 469/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DAPAR 1.28.5  (landing page)
Samuel Wieczorek
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/DAPAR
git_branch: RELEASE_3_15
git_last_commit: d484403
git_last_commit_date: 2022-07-14 00:42:40 -0400 (Thu, 14 Jul 2022)
nebbiolo1Linux (Ubuntu 20.04.5 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
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: DAPAR
Version: 1.28.5
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_1.28.5.tar.gz
StartedAt: 2022-10-19 01:17:06 -0400 (Wed, 19 Oct 2022)
EndedAt: 2022-10-19 01:40:51 -0400 (Wed, 19 Oct 2022)
EllapsedTime: 1424.6 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_1.28.5.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/DAPAR.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DAPAR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DAPAR’ version ‘1.28.5’
* 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 ‘build’ 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 R 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 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
GetIndices_MetacellFiltering: no visible global function definition for
  ‘tsop’
aggregateIterParallel: no visible binding for global variable ‘cond’
averageIntensities: no visible binding for global variable ‘condition’
averageIntensities: no visible binding for global variable ‘feature’
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’
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<-’
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
  adjusted_pvalues cond condition feature g input layout_nicely nodes<-
  par str_c textGOParams tsop x y
Consider adding
  importFrom("graphics", "par")
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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                    user  system elapsed
wrapper.compareNormalizationD_HC 560.787 270.442 823.381
metacombine                       27.710   7.206  34.454
wrapper.dapar.impute.mi           27.137   1.651  28.712
barplotEnrichGO_HC                16.677   3.018  19.629
barplotGroupGO_HC                 10.182   0.961  11.126
enrich_GO                          9.239   0.928  10.156
group_GO                           9.243   0.899  10.115
scatterplotEnrichGO_HC             9.135   0.805   9.918
densityPlotD_HC                    5.876   2.467   8.065
formatPHResults                    6.617   1.132   7.690
wrapper.CVDistD_HC                 4.862   2.801   7.519
postHocTest                        6.307   1.096   7.422
CVDistD_HC                         5.885   0.137   6.038
wrapperRunClustering               4.567   0.894   6.510
mvImage                            5.118   0.308   5.418
AggregateMetacell                  5.155   0.162   5.327
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.15-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/4.2/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
** installing vignettes
** 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 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

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 1.28.5.

  To get started, visit
    http://www.prostar-proteomics.org/


> 
> test_check("DAPAR")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
> 
> proc.time()
   user  system elapsed 
 14.560   0.539  15.099 

Example timings

DAPAR.Rcheck/DAPAR-Ex.timings

nameusersystemelapsed
AggregateMetacell5.1550.1625.327
BuildAdjacencyMatrix0.8570.0070.865
BuildColumnToProteinDataset2.2220.0142.239
BuildColumnToProteinDataset_par2.3240.1602.377
BuildMetaCell1.8160.2122.031
CVDistD_HC5.8850.1376.038
CountPep0.8470.0070.855
ExtendPalette0.0500.0020.052
GOAnalysisSave000
GetCC2.3330.0182.355
GetColorsForConditions0.7500.0040.755
GetDetailedNbPeptides0.7910.0050.797
GetDetailedNbPeptidesUsed0.0010.0000.001
GetIndices_BasedOnConditions0.7980.0060.806
GetIndices_MetacellFiltering0.7870.0060.794
GetIndices_WholeLine0.8080.0060.815
GetIndices_WholeMatrix0.7820.0060.789
GetKeyId0.7850.0070.792
GetMatAdj0.8010.0050.808
GetMetacell000
GetNbPeptidesUsed0.7940.0050.800
GetTypeofData0.7410.0050.748
Get_AllComparisons0.5140.0070.523
GlobalQuantileAlignment0.8470.0080.886
GraphPepProt0.8290.0070.855
LH0000
LH0.lm0.0000.0010.001
LH1000
LH1.lm000
LOESS1.9360.0221.964
MeanCentering0.7370.0070.744
MetaCellFiltering0.8320.0100.843
MetacellFilteringScope000
Metacell_generic0.7970.0180.815
Metacell_maxquant0.7570.0130.770
Metacell_proline0.7410.0150.757
NumericalFiltering1.3800.0091.391
NumericalgetIndicesOfLinesToRemove0.7200.0040.726
QuantileCentering0.7390.0040.744
SetCC1.9750.0101.988
SetMatAdj0.8070.0050.813
Set_POV_MEC_tags0.8120.0050.818
StringBasedFiltering0.8270.0060.833
StringBasedFiltering20.8390.0050.844
SumByColumns3.3520.0223.382
SymFilteringOperators000
UpdateMetacell0.0000.0000.001
aggregateIter2.2630.0082.273
aggregateIterParallel2.4590.1142.544
aggregateMean2.3620.1192.483
aggregateSum3.6170.0163.637
aggregateTopn2.1320.0132.146
averageIntensities0.9580.1411.164
barplotEnrichGO_HC16.677 3.01819.629
barplotGroupGO_HC10.182 0.96111.126
boxPlotD_HC0.4720.1020.566
buildGraph1.8620.0471.907
check.conditions0.7440.0060.749
check.design0.7380.0060.745
checkClusterability0.3920.0460.433
classic1wayAnova2.6940.4273.109
compareNormalizationD_HC0.2980.0610.356
compute_t_tests2.0300.4162.442
corrMatrixD_HC0.9300.0791.008
createMSnset3.1260.2333.345
dapar_hc_ExportMenu0.2460.1350.385
dapar_hc_chart0.0980.0460.143
deleteLinesFromIndices0.8440.0280.870
densityPlotD_HC5.8762.4678.065
diffAnaComputeFDR0.7710.1450.905
diffAnaGetSignificant0.5510.1040.645
diffAnaSave0.5090.0960.594
diffAnaVolcanoplot0.3320.0410.370
diffAnaVolcanoplot_rCharts0.7600.1760.922
display.CC.visNet2.1140.0992.226
enrich_GO 9.239 0.92810.156
finalizeAggregation000
findMECBlock0.8260.0210.846
formatLimmaResult1.1640.0491.211
formatPHResults6.6171.1327.690
fudge2LRT000
get.pep.prot.cc1.6570.0231.681
getIndicesConditions0.7530.0060.760
getIndicesOfLinesToRemove0.7760.0170.791
getListNbValuesInLines0.7230.0050.728
getNumberOf0.7570.0160.772
getNumberOfEmptyLines0.8130.0100.823
getPourcentageOfMV0.7570.0160.773
getProcessingInfo0.7140.0050.720
getProteinsStats0.8230.0210.844
getQuantile4Imp0.2470.0100.257
getTextForAggregation0.0000.0000.001
getTextForAnaDiff0.0000.0010.001
getTextForFiltering0.0010.0000.000
getTextForGOAnalysis0.0010.0010.000
getTextForHypothesisTest0.0000.0000.001
getTextForNewDataset0.0030.0010.004
getTextForNormalization0.0010.0000.001
getTextForpeptideImputation000
getTextForproteinImputation000
group_GO 9.243 0.89910.115
hc_logFC_DensityPlot1.2610.5081.714
hc_mvTypePlot22.5970.4883.036
heatmapD1.1850.0611.246
heatmapForMissingValues0.3510.0350.386
histPValue_HC0.4460.0990.548
impute.pa20.8740.0520.935
inner.aggregate.iter0.8680.0400.908
inner.aggregate.topn0.7930.0180.810
inner.mean0.8330.0220.856
inner.sum0.7750.0180.793
limmaCompleteTest3.2820.1283.399
listSheets0.0000.0010.000
make.contrast0.7580.0060.765
make.design.10.7610.0060.767
make.design.20.7560.0060.762
make.design.30.7470.0050.753
make.design0.7480.0060.755
match.metacell0.8530.0220.874
metacell.def0.0090.0030.011
metacellHisto_HC0.8610.0560.915
metacellPerLinesHistoPerCondition_HC1.0730.1331.253
metacellPerLinesHisto_HC0.8670.0710.950
metacombine27.710 7.20634.454
mvImage5.1180.3085.418
my_hc_ExportMenu0.2380.1390.374
my_hc_chart0.2470.1440.388
nonzero0.0270.0010.028
normalizeMethods.dapar0.0000.0000.001
pepa.test0.7760.0170.793
plotJitter1.7170.0411.759
plotJitter_rCharts1.7060.0811.785
plotPCA_Eigen0.8810.0430.922
plotPCA_Eigen_hc0.7540.0050.760
plotPCA_Ind0.7740.0080.796
plotPCA_Var0.7500.0060.757
postHocTest6.3071.0967.422
proportionConRev_HC0.0750.0470.123
rbindMSnset0.9150.0630.975
reIntroduceMEC0.9340.0630.995
readExcel000
removeLines0.8380.0310.866
samLRT000
saveParameters0.7610.0070.769
scatterplotEnrichGO_HC9.1350.8059.918
search.metacell.tags0.0180.0040.023
splitAdjacencyMat0.8290.0170.847
test.design0.9050.0090.915
translatedRandomBeta0.0040.0050.009
univ_AnnotDbPkg0.2680.0570.324
violinPlotD0.4910.0230.515
visualizeClusters2.3570.4362.748
vsn2.0540.0222.089
wrapper.CVDistD_HC4.8622.8017.519
wrapper.compareNormalizationD_HC560.787270.442823.381
wrapper.corrMatrixD_HC0.9000.0750.970
wrapper.dapar.impute.mi27.137 1.65128.712
wrapper.heatmapD1.0480.0401.089
wrapper.impute.KNN0.7930.0300.822
wrapper.impute.detQuant1.1380.1211.248
wrapper.impute.fixedValue0.9230.0620.980
wrapper.impute.mle0.8030.0320.833
wrapper.impute.pa0.2910.0380.328
wrapper.impute.pa20.8420.0550.897
wrapper.impute.slsa1.0930.0631.152
wrapper.mvImage0.3380.0450.379
wrapper.normalizeD0.7770.0080.789
wrapper.pca0.3310.0420.378
wrapperCalibrationPlot0.3920.0480.511
wrapperClassic1wayAnova3.7220.4744.978
wrapperRunClustering4.5670.8946.510
write.excel1.5530.2122.090
writeMSnsetToCSV0.8340.0301.007
writeMSnsetToExcel1.9410.3572.395