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This page was generated on 2021-07-30 15:06:20 -0400 (Fri, 30 Jul 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 1.24.7  (landing page)
Samuel Wieczorek
Snapshot Date: 2021-07-29 04:50:02 -0400 (Thu, 29 Jul 2021)
URL: https://git.bioconductor.org/packages/DAPAR
Branch: RELEASE_3_13
Last Commit: 0ea4e30
Last Changed Date: 2021-07-26 01:17:43 -0400 (Mon, 26 Jul 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  YES
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  YES

Summary

Package: DAPAR
Version: 1.24.7
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_1.24.7.tar.gz
StartedAt: 2021-07-29 17:43:46 -0400 (Thu, 29 Jul 2021)
EndedAt: 2021-07-29 17:51:18 -0400 (Thu, 29 Jul 2021)
EllapsedTime: 451.7 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_1.24.7.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 ‘1.24.7’
* 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
AggregateMetacell        16.226  3.915  19.766
CVDistD_HC                7.856  5.310  12.618
checkClusterability       4.989  2.575   7.285
formatPHResults           5.718  1.019   6.688
wrapper.CVDistD_HC        4.045  2.647   6.396
compareNormalizationD_HC  4.868  1.803   6.490
postHocTest               5.624  0.985   6.527
densityPlotD_HC           4.632  1.892   6.374
get.pep.prot.cc           4.764  0.622   5.380
* 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 
 13.562   0.815  14.363 

Example timings

DAPAR.Rcheck/DAPAR-Ex.timings

nameusersystemelapsed
AggregateMetacell16.226 3.91519.766
BuildAdjacencyMatrix0.4380.0180.456
BuildColumnToProteinDataset2.0060.4172.392
BuildColumnToProteinDataset_par0.0000.0010.000
BuildMetaCell1.5190.1141.628
CVDistD_HC 7.856 5.31012.618
CountPep0.4620.0220.484
ExtendPalette0.0600.0150.075
GetCC2.4360.1062.545
GetColorsForConditions0.2920.0030.296
GetDetailedNbPeptides0.3240.0060.330
GetIndices_MetacellFiltering0.3000.0120.312
GetIndices_WholeLine0.3870.0090.396
GetIndices_WholeMatrix0.3970.0090.406
GetMatAdj0.9170.0330.950
Get_AllComparisons0.3670.0340.399
GlobalQuantileAlignment0.3270.0040.331
GraphPepProt0.3250.0060.332
LOESS1.3270.0221.350
MeanCentering0.3430.0040.347
MetaCellFiltering0.4390.0190.458
Metacell_generic0.6720.0540.721
Metacell_maxquant0.7040.0610.761
Metacell_proline0.0010.0000.001
NumericalFiltering0.4160.0170.431
NumericalgetIndicesOfLinesToRemove0.3870.0060.393
QuantileCentering0.3550.0060.361
SetCC2.6200.0892.705
SetMatAdj0.4210.0110.432
Set_POV_MEC_tags0.4350.0200.453
StringBasedFiltering0.4630.0160.479
StringBasedFiltering20.3930.0110.404
SumByColumns2.9000.1933.077
aggregateIter2.0140.4032.372
aggregateIterParallel0.0000.0010.001
aggregateMean2.1410.4022.498
aggregateSum1.9140.3672.238
aggregateTopn0.0000.0010.001
averageIntensities0.3640.0570.420
boxPlotD_HC0.5590.2010.749
buildGraph1.3990.0521.450
check.conditions0.3420.0020.345
check.design0.3740.0030.377
checkClusterability4.9892.5757.285
classic1wayAnova2.4220.3452.747
compareNormalizationD_HC4.8681.8036.490
compute_t_tests1.8180.3532.132
corrMatrixD_HC0.5000.1200.619
createMSnset2.6610.1482.797
dapar_hc_ExportMenu0.2100.1620.373
dapar_hc_chart0.0870.0610.150
deleteLinesFromIndices0.3920.0110.404
densityPlotD_HC4.6321.8926.374
diffAnaComputeFDR0.5990.0840.681
diffAnaGetSignificant0.4120.0400.453
diffAnaSave0.3730.0350.407
diffAnaVolcanoplot0.2280.0210.248
diffAnaVolcanoplot_rCharts0.0010.0010.001
display.CC.visNet1.5800.1191.701
enrich_GO000
findMECBlock0.3500.0090.361
formatLimmaResult0.2070.0180.226
formatPHResults5.7181.0196.688
get.pep.prot.cc4.7640.6225.380
getIndicesConditions0.3140.0030.318
getIndicesOfLinesToRemove0.3890.0060.395
getListNbValuesInLines0.3630.0040.368
getNumberOf0.3640.0060.369
getNumberOfEmptyLines0.4390.0080.445
getPourcentageOfMV0.3740.0070.381
getProcessingInfo0.3750.0030.378
getProteinsStats0.3370.0080.345
getQuantile4Imp0.2680.0040.272
getTextForAggregation0.0000.0010.001
getTextForAnaDiff0.0010.0010.001
getTextForGOAnalysis0.0000.0010.001
getTextForHypothesisTest0.0000.0010.001
getTextForNewDataset0.0030.0010.002
getTextForNormalization0.0010.0000.000
getTextForpeptideImputation0.0010.0000.001
getTextForproteinImputation0.0010.0000.001
group_GO0.0000.0010.000
hc_logFC_DensityPlot1.7240.7072.363
hc_mvTypePlot21.9060.6702.509
heatmapD0.0010.0010.001
heatmapForMissingValues0.2390.0220.259
histPValue_HC0.3150.0810.399
impute.pa20.4580.0290.484
limmaCompleteTest2.6770.1002.769
make.contrast0.3720.0050.376
make.design.10.3900.0040.394
make.design.2000
make.design.30.3390.0050.344
make.design0.3140.0040.318
match.metacell0.3620.0080.369
metacellHisto_HC0.4730.0760.550
metacellPerLinesHistoPerCondition_HC0.6440.1380.784
metacellPerLinesHisto_HC0.4030.0720.477
metacombine0.0000.0010.000
mvImage4.2260.2494.455
my_hc_ExportMenu0.2410.1600.403
my_hc_chart0.2200.1620.407
nonzero0.0210.0020.023
plotJitter1.3510.0711.423
plotPCA_Eigen0.2810.0030.284
plotPCA_Eigen_hc0.3210.0030.325
plotPCA_Ind0.3540.0040.358
plotPCA_Var0.3290.0030.332
postHocTest5.6240.9856.527
proportionConRev_HC0.0650.0640.137
rbindMSnset0.4580.0220.483
reIntroduceMEC0.4730.0330.504
removeLines0.4490.0120.461
saveParameters0.3650.0040.370
search.metacell.tags0.0140.0040.018
test.design0.3360.0030.339
translatedRandomBeta0.0050.0130.018
violinPlotD0.4320.0230.457
visualizeClusters2.0260.3742.460
vsn0.6800.0160.695
wrapper.CVDistD_HC4.0452.6476.396
wrapper.compareNormalizationD_HC0.3570.0040.360
wrapper.corrMatrixD_HC0.5280.0790.608
wrapper.dapar.impute.mi0.0000.0010.001
wrapper.heatmapD0.0000.0010.001
wrapper.impute.KNN0.4700.0160.486
wrapper.impute.detQuant0.6540.0790.725
wrapper.impute.fixedValue0.5070.0310.538
wrapper.impute.mle0.4100.0150.423
wrapper.impute.pa0.3650.0180.381
wrapper.impute.pa20.4040.0280.429
wrapper.impute.slsa0.6840.0400.721
wrapper.mvImage0.1800.0170.195
wrapper.normalizeD0.3090.0030.312
wrapper.pca0.1900.0140.204
wrapperCalibrationPlot0.2120.0180.230
wrapperClassic1wayAnova3.0510.5163.546
wrapperRunClustering3.5090.7444.195
write.excel0.8400.1300.962
writeMSnsetToCSV0.0000.0000.001
writeMSnsetToExcel000