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This page was generated on 2022-01-26 13:07:52 -0500 (Wed, 26 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4080
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4141
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 machv2


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? here 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 450/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DAPAR 1.26.1  (landing page)
Samuel Wieczorek
Snapshot Date: 2022-01-25 01:55:07 -0500 (Tue, 25 Jan 2022)
git_url: https://git.bioconductor.org/packages/DAPAR
git_branch: RELEASE_3_14
git_last_commit: 9232810
git_last_commit_date: 2021-11-22 00:55:42 -0500 (Mon, 22 Nov 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: DAPAR
Version: 1.26.1
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_1.26.1.tar.gz
StartedAt: 2022-01-25 12:00:58 -0500 (Tue, 25 Jan 2022)
EndedAt: 2022-01-25 12:09:19 -0500 (Tue, 25 Jan 2022)
EllapsedTime: 501.5 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_1.26.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/DAPAR.Rcheck’
* using R version 4.1.2 (2021-11-01)
* 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 ‘1.26.1’
* 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 ... NOTE
Namespaces in Imports field not imported from:
  ‘Cairo’ ‘DAPARdata’ ‘clusterProfiler’ ‘igraph’ ‘knitr’ ‘lattice’
  ‘norm’ ‘pcaMethods’ ‘png’ ‘scales’ ‘siggenes’ ‘tidyverse’ ‘tmvtnorm’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
heatmapForMissingValues: warning in axis(1, 1:nc, label = labCol, las =
  2, line = -0.5 + offsetCol, tick = 0, cex.axis = cexCol, hadj = NA,
  padj = 0): partial argument match of 'label' to 'labels'
heatmapForMissingValues: warning in axis(1, 1:nc, label = rep("", nc),
  las = 2, tick = 0): partial argument match of 'label' to 'labels'
heatmapForMissingValues: warning in axis(4, iy, label = labRow, las =
  5, line = -0.5 + offsetRow, tick = 0, cex.axis = cexRow, hadj = 0,
  padj = NA): partial argument match of 'label' to 'labels'
heatmapForMissingValues: warning in axis(4, iy, label = rep("", nr),
  las = 2, line = -0.5, tick = 0): partial argument match of 'label' to
  'labels'
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’
averageIntensities: no visible binding for global variable ‘intensity’
barplotEnrichGO_HC : <anonymous>: no visible global function definition
  for ‘last’
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’
enrich_GO: no visible global function definition for ‘bitr’
enrich_GO: no visible global function definition for ‘enrichGO’
getTextForGOAnalysis: no visible binding for global variable
  ‘textGOParams’
getTextForGOAnalysis: no visible binding for global variable ‘input’
group_GO: no visible global function definition for ‘bitr’
group_GO: no visible global function definition for ‘groupGO’
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 global function definition for ‘desc’
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’
wrapperClassic1wayAnova: no visible binding for global variable
  ‘post_hoc’
wrapperRunClustering: no visible global function definition for ‘str_c’
Undefined global functions or variables:
  A B Condition FDR_threshold P.Value Pr(>F)1 adjusted_pvalues bitr
  cond condition desc enrichGO feature g groupGO input intensity last
  layout_nicely nodes<- post_hoc str_c textGOParams tsop x y
* 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
AggregateMetacell        16.791  3.882  20.280
CVDistD_HC                8.735  5.350  13.520
checkClusterability       5.022  2.488   7.219
postHocTest               6.251  0.986   7.128
formatPHResults           6.247  0.984   7.119
wrapper.CVDistD_HC        4.347  2.699   6.767
compareNormalizationD_HC  4.941  1.756   6.503
get.pep.prot.cc           5.897  0.714   6.605
densityPlotD_HC           4.719  1.750   6.265
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.14-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/4.1/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 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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)
> 
> test_check("DAPAR")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
> 
> proc.time()
   user  system elapsed 
 14.662   0.847  15.488 

Example timings

DAPAR.Rcheck/DAPAR-Ex.timings

nameusersystemelapsed
AggregateMetacell16.791 3.88220.280
BuildAdjacencyMatrix0.5300.0180.548
BuildColumnToProteinDataset2.1920.3932.551
BuildColumnToProteinDataset_par000
BuildMetaCell1.0460.1021.145
CVDistD_HC 8.735 5.35013.520
CountPep0.7030.0250.730
ExtendPalette0.0570.0170.074
GetCC2.8870.1153.008
GetColorsForConditions0.4870.0050.494
GetDetailedNbPeptides0.5100.0110.523
GetIndices_MetacellFiltering0.5260.0130.540
GetIndices_WholeLine0.5040.0130.516
GetIndices_WholeMatrix0.5030.0120.515
GetMatAdj0.6570.0300.687
Get_AllComparisons0.4210.0480.468
GlobalQuantileAlignment0.4500.0060.457
GraphPepProt0.4710.0110.481
LOESS1.5930.0201.613
MeanCentering0.4690.0070.477
MetaCellFiltering0.6170.0180.635
Metacell_generic0.8810.0720.948
Metacell_maxquant0.7050.0700.771
Metacell_proline0.0000.0010.001
NumericalFiltering0.5780.0200.598
NumericalgetIndicesOfLinesToRemove0.5200.0080.529
QuantileCentering0.4710.0080.480
SetCC2.4710.1052.577
SetMatAdj0.6190.0260.645
Set_POV_MEC_tags0.4440.0210.464
StringBasedFiltering0.5720.0160.587
StringBasedFiltering20.4970.0120.509
SumByColumns3.0880.1973.268
aggregateIter2.2830.4282.672
aggregateIterParallel0.0010.0000.001
aggregateMean2.1280.4152.509
aggregateSum3.8600.7854.555
aggregateTopn0.0000.0010.001
averageIntensities0.3280.0580.382
boxPlotD_HC0.6690.1970.854
buildGraph1.4990.0561.552
check.conditions0.4120.0040.415
check.design0.4750.0040.479
checkClusterability5.0222.4887.219
classic1wayAnova2.4180.3122.696
compareNormalizationD_HC4.9411.7566.503
compute_t_tests1.8600.3802.212
corrMatrixD_HC0.6590.0820.738
createMSnset2.9320.1573.077
dapar_hc_ExportMenu0.2460.1780.496
dapar_hc_chart0.1010.0590.158
deleteLinesFromIndices1.1070.0111.119
densityPlotD_HC4.7191.7506.265
diffAnaComputeFDR0.6610.0790.736
diffAnaGetSignificant0.3770.0350.409
diffAnaSave0.3550.0330.386
diffAnaVolcanoplot0.2530.0230.279
diffAnaVolcanoplot_rCharts0.0000.0010.001
display.CC.visNet1.7090.1121.831
enrich_GO000
findMECBlock0.5080.0090.517
formatLimmaResult0.2240.0160.240
formatPHResults6.2470.9847.119
get.pep.prot.cc5.8970.7146.605
getIndicesConditions0.4570.0050.463
getIndicesOfLinesToRemove0.4610.0060.468
getListNbValuesInLines0.4920.0040.497
getNumberOf0.4690.0070.476
getNumberOfEmptyLines0.5290.0080.536
getPourcentageOfMV0.5310.0100.540
getProcessingInfo0.4200.0040.424
getProteinsStats0.5240.0120.581
getQuantile4Imp0.3830.0040.387
getTextForAggregation0.0000.0010.001
getTextForAnaDiff0.0000.0010.001
getTextForGOAnalysis0.0010.0010.001
getTextForHypothesisTest0.0000.0010.001
getTextForNewDataset0.0040.0000.004
getTextForNormalization0.0010.0000.001
getTextForpeptideImputation0.0000.0000.001
getTextForproteinImputation0.0010.0000.001
group_GO0.0010.0000.001
hc_logFC_DensityPlot1.7870.6882.402
hc_mvTypePlot22.1240.6692.720
heatmapD0.0000.0000.001
heatmapForMissingValues0.2610.0190.280
histPValue_HC0.3180.0770.394
impute.pa20.4690.0290.494
limmaCompleteTest2.7490.1082.846
make.contrast0.3960.0040.401
make.design.10.3090.0030.313
make.design.20.0010.0010.001
make.design.30.4020.0080.410
make.design0.4940.0040.500
match.metacell0.5090.0090.518
metacellHisto_HC0.5660.0710.636
metacellPerLinesHistoPerCondition_HC0.6910.1310.817
metacellPerLinesHisto_HC0.6240.0700.692
metacombine0.0000.0010.001
mvImage4.4570.2604.695
my_hc_ExportMenu0.2780.1730.447
my_hc_chart0.2460.1670.411
nonzero0.0270.0020.028
plotJitter1.5720.0521.624
plotPCA_Eigen0.3220.0040.325
plotPCA_Eigen_hc0.4600.0050.468
plotPCA_Ind0.4680.0040.473
plotPCA_Var0.4900.0050.496
postHocTest6.2510.9867.128
proportionConRev_HC0.0830.0580.140
rbindMSnset0.6060.0200.625
reIntroduceMEC0.6370.0360.670
removeLines0.5240.0150.541
saveParameters0.4590.0060.464
search.metacell.tags0.0160.0050.019
test.design0.4590.0040.463
translatedRandomBeta0.0060.0220.028
violinPlotD0.4440.0270.470
visualizeClusters2.0820.3932.434
vsn0.8120.0190.831
wrapper.CVDistD_HC4.3472.6996.767
wrapper.compareNormalizationD_HC0.5220.0050.529
wrapper.corrMatrixD_HC0.6760.0840.757
wrapper.dapar.impute.mi0.0000.0010.001
wrapper.heatmapD0.0000.0010.001
wrapper.impute.KNN0.5170.0150.533
wrapper.impute.detQuant0.7520.0980.854
wrapper.impute.fixedValue0.5990.0340.629
wrapper.impute.mle0.5870.0160.601
wrapper.impute.pa0.5590.0200.579
wrapper.impute.pa20.4930.0290.519
wrapper.impute.slsa0.8410.0520.905
wrapper.mvImage0.2190.0180.237
wrapper.normalizeD0.4740.0050.479
wrapper.pca0.2150.0150.228
wrapperCalibrationPlot0.2350.0190.254
wrapperClassic1wayAnova3.3850.4803.811
wrapperRunClustering3.9160.7444.573
write.excel1.0010.1351.121
writeMSnsetToCSV0.0000.0010.001
writeMSnsetToExcel000