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This page was generated on 2022-01-24 13:04:58 -0500 (Mon, 24 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 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? 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: 2022-01-23 01:55:04 -0500 (Sun, 23 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: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:DAPAR.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings DAPAR_1.26.1.tar.gz
StartedAt: 2022-01-23 07:12:42 -0500 (Sun, 23 Jan 2022)
EndedAt: 2022-01-23 07:18:25 -0500 (Sun, 23 Jan 2022)
EllapsedTime: 343.3 seconds
RetCode: 0
Status:   OK  
CheckDir: DAPAR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:DAPAR.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings DAPAR_1.26.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/DAPAR.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-pc-linux-gnu (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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
AggregateMetacell 11.561  1.740  12.920
CVDistD_HC         5.999  2.096   7.506
get.pep.prot.cc    6.260  1.060   7.307
* 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
  ‘/home/biocbuild/bbs-3.14-bioc/meat/DAPAR.Rcheck/00check.log’
for details.



Installation output

DAPAR.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL DAPAR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/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-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)
> 
> test_check("DAPAR")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
> 
> proc.time()
   user  system elapsed 
  9.682   0.508  10.163 

Example timings

DAPAR.Rcheck/DAPAR-Ex.timings

nameusersystemelapsed
AggregateMetacell11.561 1.74012.920
BuildAdjacencyMatrix0.4840.0150.499
BuildColumnToProteinDataset1.6420.1441.744
BuildColumnToProteinDataset_par0.0000.0000.001
BuildMetaCell1.0140.0481.061
CVDistD_HC5.9992.0967.506
CountPep0.5810.0100.590
ExtendPalette0.0670.0200.086
GetCC2.6250.1762.794
GetColorsForConditions0.2650.0000.265
GetDetailedNbPeptides0.2890.0000.289
GetIndices_MetacellFiltering0.2780.0050.283
GetIndices_WholeLine0.2830.0030.285
GetIndices_WholeMatrix0.2710.0160.286
GetMatAdj0.3620.0030.363
Get_AllComparisons0.2510.0230.271
GlobalQuantileAlignment0.3410.0070.347
GraphPepProt0.3090.0030.311
LOESS1.0760.0051.081
MeanCentering0.3040.0030.307
MetaCellFiltering0.3340.0160.348
Metacell_generic0.5460.0150.556
Metacell_maxquant1.1080.0791.183
Metacell_proline000
NumericalFiltering0.3190.0000.317
NumericalgetIndicesOfLinesToRemove0.2720.0000.271
QuantileCentering0.3070.0020.308
SetCC2.8050.0962.893
SetMatAdj0.3450.0070.352
Set_POV_MEC_tags0.2930.0040.295
StringBasedFiltering0.2960.0070.302
StringBasedFiltering20.2860.0120.297
SumByColumns1.1950.0921.275
aggregateIter1.2460.1601.363
aggregateIterParallel000
aggregateMean1.4410.1401.536
aggregateSum1.7440.2131.891
aggregateTopn000
averageIntensities0.1940.0160.208
boxPlotD_HC0.3740.0540.419
buildGraph1.6380.1471.785
check.conditions0.3390.0000.339
check.design0.2690.0030.271
checkClusterability3.9430.7664.419
classic1wayAnova1.4920.1211.584
compareNormalizationD_HC3.4300.5823.840
compute_t_tests1.0400.1691.173
corrMatrixD_HC0.3970.0190.412
createMSnset2.1960.0742.256
dapar_hc_ExportMenu0.2030.0290.229
dapar_hc_chart0.0450.0160.060
deleteLinesFromIndices0.3440.0030.347
densityPlotD_HC3.0500.5603.509
diffAnaComputeFDR0.5820.0230.602
diffAnaGetSignificant0.3090.0200.325
diffAnaSave0.2910.0120.299
diffAnaVolcanoplot0.2090.0120.220
diffAnaVolcanoplot_rCharts0.0000.0000.001
display.CC.visNet1.6440.0991.735
enrich_GO000
findMECBlock0.4380.0070.445
formatLimmaResult0.1910.0080.198
formatPHResults4.2390.3014.454
get.pep.prot.cc6.2601.0607.307
getIndicesConditions0.2480.0030.253
getIndicesOfLinesToRemove0.2720.0000.272
getListNbValuesInLines0.2540.0000.253
getNumberOf0.2670.0000.266
getNumberOfEmptyLines0.2720.0090.281
getPourcentageOfMV0.2880.0030.290
getProcessingInfo0.2530.0040.257
getProteinsStats0.2920.0000.291
getQuantile4Imp0.2850.0150.299
getTextForAggregation000
getTextForAnaDiff0.0000.0000.001
getTextForGOAnalysis0.0000.0000.001
getTextForHypothesisTest000
getTextForNewDataset0.0030.0000.003
getTextForNormalization000
getTextForpeptideImputation0.0010.0000.000
getTextForproteinImputation0.0000.0000.001
group_GO0.0000.0000.001
hc_logFC_DensityPlot0.9910.1771.111
hc_mvTypePlot21.3400.2001.471
heatmapD000
heatmapForMissingValues0.2420.0080.247
histPValue_HC0.2570.0160.270
impute.pa20.4440.0150.456
limmaCompleteTest1.6360.0271.647
make.contrast0.2500.0080.258
make.design.10.2600.0030.264
make.design.2000
make.design.30.2620.0000.262
make.design0.2520.0030.255
match.metacell0.2740.0040.278
metacellHisto_HC0.3160.0230.337
metacellPerLinesHistoPerCondition_HC0.5890.0230.608
metacellPerLinesHisto_HC0.4380.0080.443
metacombine000
mvImage2.8030.0662.841
my_hc_ExportMenu0.1870.0330.215
my_hc_chart0.1930.0330.221
nonzero0.0670.0000.068
plotJitter1.5410.0131.550
plotPCA_Eigen0.390.000.39
plotPCA_Eigen_hc0.250.000.25
plotPCA_Ind0.2420.0000.242
plotPCA_Var0.4090.0010.411
postHocTest4.0580.3034.257
proportionConRev_HC0.0530.0120.064
rbindMSnset0.5540.0030.555
reIntroduceMEC0.5310.0080.534
removeLines0.4520.0000.450
saveParameters0.3690.0000.369
search.metacell.tags0.0110.0000.011
test.design0.3810.0020.382
translatedRandomBeta0.0050.0000.005
violinPlotD0.4660.0070.472
visualizeClusters1.1930.0791.236
vsn0.4830.0000.482
wrapper.CVDistD_HC2.5120.8323.088
wrapper.compareNormalizationD_HC0.3200.0000.319
wrapper.corrMatrixD_HC0.3590.0230.380
wrapper.dapar.impute.mi000
wrapper.heatmapD000
wrapper.impute.KNN0.2960.0030.299
wrapper.impute.detQuant0.4590.0200.472
wrapper.impute.fixedValue0.3300.0120.340
wrapper.impute.mle0.3430.0120.353
wrapper.impute.pa0.4850.0080.492
wrapper.impute.pa20.3180.0150.331
wrapper.impute.slsa0.4360.0000.433
wrapper.mvImage0.1080.0120.118
wrapper.normalizeD0.2690.0000.269
wrapper.pca0.1170.0030.118
wrapperCalibrationPlot0.1440.0000.142
wrapperClassic1wayAnova1.7080.1141.780
wrapperRunClustering2.1030.1982.229
write.excel0.5640.0450.597
writeMSnsetToCSV000
writeMSnsetToExcel000