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This page was generated on 2021-06-17 02:39:06 -0400 (Thu, 17 Jun 2021).

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 442/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DAPAR 1.24.4  (landing page)
Samuel Wieczorek
Snapshot Date: 2021-06-15 06:50:12 -0400 (Tue, 15 Jun 2021)
URL: https://git.bioconductor.org/packages/DAPAR
Branch: RELEASE_3_13
Last Commit: 12b8d14
Last Changed Date: 2021-06-08 22:14:55 -0400 (Tue, 08 Jun 2021)
nebbiolo1Linux (Ubuntu 20.04.2 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: 1.24.4
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:DAPAR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings DAPAR_1.24.4.tar.gz
StartedAt: 2021-06-15 17:56:46 -0400 (Tue, 15 Jun 2021)
EndedAt: 2021-06-15 18:03:41 -0400 (Tue, 15 Jun 2021)
EllapsedTime: 414.9 seconds
RetCode: 0
Status:   OK  
CheckDir: DAPAR.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:DAPAR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings DAPAR_1.24.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/DAPAR.Rcheck’
* using R version 4.1.0 (2021-05-18)
* 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 ‘1.24.4’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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
CVDistD_HC               8.632  5.469  13.581
checkClusterability      4.945  2.478   7.138
wrapper.CVDistD_HC       4.197  2.672   6.579
formatPHResults          5.859  0.941   6.699
postHocTest              5.787  0.938   6.628
compareNormalizationD_HC 4.697  1.734   6.298
densityPlotD_HC          4.619  1.774   6.201
AggregateMetacell        4.939  0.542   5.440
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/DAPAR.Rcheck/00check.log’
for details.



Installation output

DAPAR.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/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 4.1.0 (2021-05-18) -- "Camp Pontanezen"
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 
 12.919   0.782  13.673 

Example timings

DAPAR.Rcheck/DAPAR-Ex.timings

nameusersystemelapsed
AggregateMetacell4.9390.5425.440
BuildAdjacencyMatrix0.3530.0150.366
BuildColumnToProteinDataset0.8470.0600.901
BuildColumnToProteinDataset_par000
BuildMetaCell0.8640.0760.937
CVDistD_HC 8.632 5.46913.581
CountPep0.5120.0230.535
ExtendPalette0.0580.0140.071
GetColorsForConditions0.3430.0030.347
GetDetailedNbPeptides0.3800.0080.387
GetIndices_MetacellFiltering0.3720.0080.380
GetIndices_WholeLine0.3910.0080.399
GetIndices_WholeMatrix0.3500.0070.358
Get_AllComparisons0.3560.0330.388
GlobalQuantileAlignment0.3310.0030.335
GraphPepProt0.4170.0080.425
LOESS1.3700.0141.385
MeanCentering0.3410.0080.348
MetaCellFiltering0.4210.0120.434
Metacell_generic0.8300.0670.893
Metacell_maxquant0.6890.0520.735
Metacell_proline0.0000.0010.001
NumericalFiltering0.4480.0170.464
NumericalgetIndicesOfLinesToRemove0.9070.0090.916
QuantileCentering0.3770.0040.381
Set_POV_MEC_tags0.3920.0090.400
StringBasedFiltering0.4400.0160.455
StringBasedFiltering20.4360.0120.447
SumByColumns2.9870.1943.176
aggregateIter1.0210.0941.107
aggregateIterParallel000
aggregateMean0.8110.0630.868
aggregateSum0.8180.0580.872
aggregateTopn000
averageIntensities0.3780.0520.427
boxPlotD_HC0.5660.1910.749
buildGraph1.7150.0411.755
check.conditions0.2550.0050.261
check.design0.3450.0030.349
checkClusterability4.9452.4787.138
classic1wayAnova2.1900.3102.471
compareNormalizationD_HC4.6971.7346.298
compute_t_tests1.7480.3752.107
corrMatrixD_HC0.5070.0880.595
createMSnset2.6900.1512.834
dapar_hc_ExportMenu0.2410.1830.433
dapar_hc_chart0.0800.0580.142
deleteLinesFromIndices0.3310.0130.345
densityPlotD_HC4.6191.7746.201
diffAnaComputeFDR0.6280.0760.700
diffAnaGetSignificant0.3950.0320.425
diffAnaSave0.3160.0290.342
diffAnaVolcanoplot0.2310.0180.248
diffAnaVolcanoplot_rCharts0.0000.0010.001
display.CC.visNet1.6460.1141.755
enrich_GO0.0000.0010.000
findMECBlock0.3670.0070.374
formatLimmaResult0.1930.0130.206
formatPHResults5.8590.9416.699
get.pep.prot.cc0.9670.0110.977
getIndicesConditions0.2850.0030.288
getIndicesOfLinesToRemove0.3960.0060.402
getListNbValuesInLines0.3180.0030.321
getNumberOf0.3160.0050.322
getNumberOfEmptyLines0.4170.0080.426
getPourcentageOfMV0.4140.0080.421
getProcessingInfo0.3110.0030.314
getProteinsStats0.4210.0090.430
getQuantile4Imp0.3390.0110.350
getTextForAggregation0.0000.0010.000
getTextForAnaDiff0.0000.0010.002
getTextForGOAnalysis0.0010.0010.001
getTextForHypothesisTest0.0000.0010.000
getTextForNewDataset0.0030.0010.004
getTextForNormalization0.0010.0000.001
getTextForpeptideImputation0.0010.0000.001
getTextForproteinImputation0.0000.0010.002
group_GO0.0010.0000.000
hc_logFC_DensityPlot1.6980.6742.309
hc_mvTypePlot21.8780.6632.477
heatmapD0.0000.0010.001
heatmapForMissingValues0.2510.0180.268
histPValue_HC0.2960.0680.366
impute.pa20.3570.0260.380
limmaCompleteTest2.6240.1062.725
make.contrast0.3650.0050.370
make.design.10.3360.0040.340
make.design.20.0010.0010.000
make.design.30.3430.0050.347
make.design0.3450.0050.350
match.metacell0.4250.0070.433
metacellHisto_HC0.4030.0570.459
metacellPerLinesHistoPerCondition_HC0.6260.1440.772
metacellPerLinesHisto_HC0.3660.0850.452
metacombine0.0000.0010.001
mvImage4.2370.2464.462
my_hc_ExportMenu0.2100.1600.376
my_hc_chart0.2130.1590.381
nonzero0.0230.0010.025
plotJitter1.4600.0431.505
plotPCA_Eigen0.3850.0040.388
plotPCA_Eigen_hc0.2870.0030.290
plotPCA_Ind0.2520.0040.255
plotPCA_Var0.3040.0030.308
postHocTest5.7870.9386.628
proportionConRev_HC0.0700.0540.130
rbindMSnset0.5040.0180.521
reIntroduceMEC0.4240.0150.438
removeLines0.3820.0120.393
saveParameters0.3480.0050.353
search.metacell.tags0.0020.0010.003
test.design0.3070.0030.310
translatedRandomBeta0.0040.0100.015
violinPlotD0.3930.0190.413
visualizeClusters1.9930.3742.326
vsn0.7330.0190.752
wrapper.CVDistD_HC4.1972.6726.579
wrapper.compareNormalizationD_HC0.3240.0040.329
wrapper.corrMatrixD_HC0.4880.0980.592
wrapper.dapar.impute.mi0.0000.0010.001
wrapper.heatmapD000
wrapper.impute.KNN0.3670.0150.385
wrapper.impute.detQuant0.5050.0250.528
wrapper.impute.fixedValue0.4520.0160.466
wrapper.impute.mle0.4170.0150.432
wrapper.impute.pa0.4210.0150.434
wrapper.impute.pa20.3110.0260.333
wrapper.impute.slsa0.3490.0140.363
wrapper.mvImage0.1750.0130.187
wrapper.normalizeD0.3190.0040.323
wrapper.pca0.1830.0150.198
wrapperCalibrationPlot0.2190.0170.236
wrapperClassic1wayAnova3.1550.4563.561
wrapperRunClustering3.8090.7594.486
writeMSnsetToCSV0.0000.0000.001
writeMSnsetToExcel0.0000.0000.001