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This page was generated on 2023-04-12 11:05:02 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
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 nebbiolo2


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 476/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DAPAR 1.30.6  (landing page)
Samuel Wieczorek
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/DAPAR
git_branch: RELEASE_3_16
git_last_commit: 3984ff9
git_last_commit_date: 2023-02-23 05:52:45 -0400 (Thu, 23 Feb 2023)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: DAPAR
Version: 1.30.6
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:DAPAR.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings DAPAR_1.30.6.tar.gz
StartedAt: 2023-04-10 20:07:33 -0400 (Mon, 10 Apr 2023)
EndedAt: 2023-04-10 20:13:08 -0400 (Mon, 10 Apr 2023)
EllapsedTime: 335.1 seconds
RetCode: 0
Status:   OK  
CheckDir: DAPAR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:DAPAR.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings DAPAR_1.30.6.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/DAPAR.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘DAPAR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DAPAR’ version ‘1.30.6’
* 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 loading without being on the library search path ... 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
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’
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 Prostar.loc
  adjusted_pvalues cond condition feature g input installed.packages
  intensity layout_nicely nodes<- par str_c textGOParams x y
Consider adding
  importFrom("graphics", "par")
  importFrom("utils", "installed.packages")
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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                   user system elapsed
wrapper.compareNormalizationD_HC 41.605 12.680  50.187
wrapper.dapar.impute.mi          12.784  0.258  12.950
barplotEnrichGO_HC               10.205  1.055  11.058
barplotGroupGO_HC                 5.700  0.298   5.954
enrich_GO                         5.332  0.270   5.549
* 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 ...
  ‘Prostar_UserManual.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.16-bioc/meat/DAPAR.Rcheck/00check.log’
for details.



Installation output

DAPAR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL DAPAR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-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
** 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 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 1.30.6.

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


> 
> test_check("DAPAR")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 14 ]
> 
> proc.time()
   user  system elapsed 
  7.911   0.467   8.374 

Example timings

DAPAR.Rcheck/DAPAR-Ex.timings

nameusersystemelapsed
AggregateMetacell1.7980.0881.886
BuildAdjacencyMatrix0.2920.0040.296
BuildColumnToProteinDataset0.8850.0720.957
BuildMetaCell0.5180.0240.543
CVDistD_HC2.2220.0642.293
CountPep0.3730.0190.394
ExtendPalette0.0260.0040.030
GOAnalysisSave000
GetCC1.7870.0481.835
GetColorsForConditions0.2340.0010.235
GetDetailedNbPeptides0.2480.0080.256
GetDetailedNbPeptidesUsed000
GetIndices_BasedOnConditions0.2550.0000.256
GetIndices_MetacellFiltering0.2590.0000.259
GetIndices_WholeLine0.2540.0000.255
GetIndices_WholeMatrix0.2510.0030.255
GetKeyId0.2490.0010.249
GetMatAdj0.2870.0040.291
GetMetacell000
GetMetacellTags0.2420.0030.245
GetNbPeptidesUsed0.2500.0010.250
GetSoftAvailables0.0010.0000.000
GetTypeofData0.2330.0000.232
Get_AllComparisons0.2290.0120.241
GlobalQuantileAlignment0.2770.0000.278
GraphPepProt0.2620.0000.262
LH0000
LH0.lm000
LH1000
LH1.lm000
LOESS0.980.021.00
MeanCentering0.2370.0080.246
MetaCellFiltering0.2890.0080.297
MetacellFilteringScope000
Metacell_DIA_NN0.4070.0200.427
Metacell_generic0.4900.0000.489
Metacell_maxquant0.3950.0120.407
Metacell_proline0.4610.0040.465
NumericalFiltering0.3690.0080.376
NumericalgetIndicesOfLinesToRemove0.3440.0000.343
QuantileCentering0.2570.0040.261
SetCC1.6980.0881.786
SetMatAdj0.2720.0030.275
Set_POV_MEC_tags0.2630.0010.263
StringBasedFiltering0.2820.0000.282
StringBasedFiltering20.2790.0000.280
SumByColumns1.0710.0191.091
SymFilteringOperators000
UpdateMetacell000
aggregateIter0.4440.0230.468
aggregateIterParallel0.0010.0000.000
aggregateMean0.3740.0130.385
aggregateSum0.3990.0000.398
aggregateTopn0.3370.0040.341
averageIntensities0.4540.0560.503
barplotEnrichGO_HC10.205 1.05511.058
barplotGroupGO_HC5.7000.2985.954
boxPlotD_HC0.2840.0280.307
buildGraph1.5620.0521.611
check.conditions0.2430.0000.243
check.design0.2420.0040.246
checkClusterability2.8930.8723.460
classic1wayAnova1.1660.1791.308
compareNormalizationD_HC0.1490.0120.160
compute_t_tests0.9110.1361.007
corrMatrixD_HC0.3180.0280.343
createMSnset1.7780.0481.809
dapar_hc_ExportMenu0.1240.0240.146
dapar_hc_chart0.0600.0080.067
deleteLinesFromIndices0.2780.0200.296
densityPlotD_HC2.6040.6012.995
diffAnaComputeFDR0.3850.0170.390
diffAnaGetSignificant0.2310.0370.257
diffAnaSave0.2250.0210.237
diffAnaVolcanoplot0.1370.0040.138
diffAnaVolcanoplot_rCharts0.3270.0620.374
display.CC.visNet1.2850.0601.336
enrich_GO5.3320.2705.549
finalizeAggregation000
findMECBlock0.2620.0080.269
formatLimmaResult0.1330.0010.130
formatPHResults3.1200.3333.343
fudge2LRT0.0000.0000.001
get.pep.prot.cc1.2640.0401.303
getIndicesConditions0.230.000.23
getIndicesOfLinesToRemove0.2410.0070.246
getListNbValuesInLines0.2350.0000.234
getNumberOf0.2600.0080.266
getNumberOfEmptyLines0.260.000.26
getPourcentageOfMV0.2560.0070.263
getProcessingInfo0.2360.0000.236
getProteinsStats0.2930.0040.295
getQuantile4Imp0.0620.0000.062
getTextForAggregation000
getTextForAnaDiff0.0000.0000.001
getTextForFiltering0.0010.0000.000
getTextForGOAnalysis000
getTextForHypothesisTest0.0000.0000.001
getTextForNewDataset0.0020.0000.002
getTextForNormalization0.0000.0000.001
getTextForpeptideImputation0.0010.0000.000
getTextForproteinImputation000
group_GO4.4840.3084.747
hc_logFC_DensityPlot0.4920.0970.548
hc_mvTypePlot20.7060.1430.812
heatmapD0.5760.0150.589
heatmapForMissingValues0.1550.0090.161
histPValue_HC0.1920.0200.205
impute.pa20.5270.0080.530
inner.aggregate.iter0.3060.0200.324
inner.aggregate.topn0.2760.0190.293
inner.mean0.2680.0090.276
inner.sum0.2720.0120.283
limmaCompleteTest1.1690.0521.210
listSheets000
make.contrast0.2560.0000.257
make.design.10.2990.0000.299
make.design.20.2860.0030.289
make.design.30.2700.0030.272
make.design0.2500.0050.254
match.metacell0.2690.0110.280
metacell.def0.0050.0010.005
metacellHisto_HC0.3480.0070.353
metacellPerLinesHistoPerCondition_HC0.4360.0240.456
metacellPerLinesHisto_HC0.3280.0120.338
metacombine0.0620.0000.061
mvImage1.8750.0681.919
my_hc_ExportMenu0.1210.0250.142
my_hc_chart0.1100.0360.143
nonzero0.0140.0080.022
normalizeMethods.dapar000
pepa.test0.2880.0040.290
pkgs.require000
plotJitter1.4000.0191.416
plotJitter_rCharts1.2130.0281.236
plotPCA_Eigen0.3180.0080.323
plotPCA_Eigen_hc0.2300.0030.233
plotPCA_Ind0.2420.0000.242
plotPCA_Var0.2370.0000.237
postHocTest2.9050.2993.111
proportionConRev_HC0.0480.0080.054
rbindMSnset0.3490.0120.357
reIntroduceMEC0.3430.0090.346
readExcel000
removeLines0.3190.0110.329
samLRT000
saveParameters0.2420.0000.242
scatterplotEnrichGO_HC4.5750.2874.820
search.metacell.tags0.0090.0000.008
splitAdjacencyMat0.3040.0040.308
test.design0.3660.0000.365
translatedRandomBeta0.0000.0030.003
univ_AnnotDbPkg0.2170.0160.232
violinPlotD0.2580.0010.256
visualizeClusters1.2830.1221.370
vsn0.4620.0040.464
wrapper.CVDistD_HC1.9420.6832.380
wrapper.compareNormalizationD_HC41.60512.68050.187
wrapper.corrMatrixD_HC0.3430.0110.349
wrapper.dapar.impute.mi12.784 0.25812.950
wrapper.heatmapD0.5200.0070.525
wrapper.impute.KNN0.2840.0070.290
wrapper.impute.detQuant0.4020.0320.423
wrapper.impute.fixedValue0.3320.0240.350
wrapper.impute.mle0.3190.0210.337
wrapper.impute.pa0.1100.0080.116
wrapper.impute.pa20.2970.0000.294
wrapper.impute.slsa0.4250.0000.420
wrapper.mvImage0.1280.0060.131
wrapper.normalizeD0.2990.0000.299
wrapper.pca0.1210.0020.121
wrapperCalibrationPlot0.1590.0040.159
wrapperClassic1wayAnova1.4550.2001.601
wrapperRunClustering1.8370.1681.947
write.excel1.5330.1611.675
writeMSnsetToCSV0.2590.0020.260
writeMSnsetToExcel0.6910.0700.732