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This page was generated on 2021-06-17 02:38:17 -0400 (Thu, 17 Jun 2021).

CHECK results for DAPAR on nebbiolo1

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: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:DAPAR.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings DAPAR_1.24.4.tar.gz
StartedAt: 2021-06-15 11:31:25 -0400 (Tue, 15 Jun 2021)
EndedAt: 2021-06-15 11:35:28 -0400 (Tue, 15 Jun 2021)
EllapsedTime: 242.8 seconds
RetCode: 0
Status:   OK  
CheckDir: DAPAR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:DAPAR.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings DAPAR_1.24.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/DAPAR.Rcheck’
* using R version 4.1.0 (2021-05-18)
* 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 ‘1.24.4’
* 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 ... 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
CVDistD_HC 3.791  1.571   4.891
* 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-3.13-bioc/meat/DAPAR.Rcheck/00check.log’
for details.



Installation output

DAPAR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL DAPAR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-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 4.1.0 (2021-05-18) -- "Camp Pontanezen"
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 
  8.335   0.467   8.775 

Example timings

DAPAR.Rcheck/DAPAR-Ex.timings

nameusersystemelapsed
AggregateMetacell2.5200.3032.781
BuildAdjacencyMatrix0.2480.0250.271
BuildColumnToProteinDataset0.4620.0400.496
BuildColumnToProteinDataset_par000
BuildMetaCell0.6100.0530.660
CVDistD_HC3.7911.5714.891
CountPep0.3370.0080.344
ExtendPalette0.0310.0080.038
GetColorsForConditions0.2040.0030.208
GetDetailedNbPeptides0.2290.0030.231
GetIndices_MetacellFiltering0.2180.0080.225
GetIndices_WholeLine0.2170.0030.220
GetIndices_WholeMatrix0.2270.0160.241
Get_AllComparisons0.2290.0150.244
GlobalQuantileAlignment0.2470.0030.251
GraphPepProt0.2220.0080.229
LOESS0.9240.0030.927
MeanCentering0.2340.0080.242
MetaCellFiltering0.2570.0160.272
Metacell_generic0.5530.0280.577
Metacell_maxquant0.4740.0110.481
Metacell_proline0.0000.0000.001
NumericalFiltering0.2550.0030.257
NumericalgetIndicesOfLinesToRemove0.2450.0160.260
QuantileCentering0.2060.0030.210
Set_POV_MEC_tags0.8690.0550.924
StringBasedFiltering0.2480.0120.259
StringBasedFiltering20.2280.0150.242
SumByColumns1.0990.0441.126
aggregateIter0.5990.0440.640
aggregateIterParallel000
aggregateMean0.4430.0200.457
aggregateSum0.4040.0280.425
aggregateTopn0.0010.0000.000
averageIntensities0.1910.0560.245
boxPlotD_HC0.3740.0620.425
buildGraph1.6730.0661.738
check.conditions0.2050.0000.205
check.design0.2060.0000.206
checkClusterability2.3020.7662.820
classic1wayAnova1.0690.1281.162
compareNormalizationD_HC2.0440.5632.438
compute_t_tests0.8670.1130.942
corrMatrixD_HC0.3120.0160.324
createMSnset1.7510.0531.792
dapar_hc_ExportMenu0.1200.0400.158
dapar_hc_chart0.0450.0080.052
deleteLinesFromIndices0.2340.0030.237
densityPlotD_HC2.0880.5282.449
diffAnaComputeFDR0.3320.0280.355
diffAnaGetSignificant0.2480.0110.256
diffAnaSave0.1780.0240.201
diffAnaVolcanoplot0.1280.0070.134
diffAnaVolcanoplot_rCharts0.0010.0010.001
display.CC.visNet1.8800.0961.970
enrich_GO0.0000.0000.001
findMECBlock0.2140.0000.214
formatLimmaResult0.1120.0030.114
formatPHResults2.8080.2893.005
get.pep.prot.cc0.8520.0170.870
getIndicesConditions0.2010.0000.201
getIndicesOfLinesToRemove0.2170.0030.219
getListNbValuesInLines0.1960.0030.200
getNumberOf0.210.000.21
getNumberOfEmptyLines0.2180.0000.218
getPourcentageOfMV0.2150.0050.219
getProcessingInfo0.1980.0000.197
getProteinsStats0.2430.0120.253
getQuantile4Imp0.2200.0070.227
getTextForAggregation000
getTextForAnaDiff0.0000.0000.001
getTextForGOAnalysis0.0000.0000.001
getTextForHypothesisTest0.0000.0000.001
getTextForNewDataset0.0010.0000.002
getTextForNormalization0.0010.0000.000
getTextForpeptideImputation000
getTextForproteinImputation000
group_GO000
hc_logFC_DensityPlot0.7660.2190.925
hc_mvTypePlot20.8980.2061.047
heatmapD000
heatmapForMissingValues0.1590.0080.166
histPValue_HC0.1960.0040.196
impute.pa20.2320.0120.241
limmaCompleteTest1.0310.0111.033
make.contrast0.2010.0020.203
make.design.10.2040.0000.204
make.design.20.0010.0000.000
make.design.30.2080.0030.211
make.design0.2300.0150.245
match.metacell0.2130.0040.216
metacellHisto_HC0.2390.0160.253
metacellPerLinesHistoPerCondition_HC0.3810.0150.393
metacellPerLinesHisto_HC0.2460.0240.269
metacombine0.0000.0000.001
mvImage1.6790.0901.749
my_hc_ExportMenu0.1100.0360.143
my_hc_chart0.1140.0200.131
nonzero0.0140.0000.014
plotJitter1.2850.0291.314
plotPCA_Eigen0.1990.0040.202
plotPCA_Eigen_hc0.1910.0030.194
plotPCA_Ind0.1930.0000.192
plotPCA_Var0.1940.0000.193
postHocTest2.7980.3323.022
proportionConRev_HC0.0320.0160.047
rbindMSnset0.2660.0070.272
reIntroduceMEC0.2590.0000.257
removeLines0.2230.0080.230
saveParameters0.1960.0080.204
search.metacell.tags0.0000.0020.002
test.design0.2000.0020.203
translatedRandomBeta0.0010.0100.010
violinPlotD0.2880.0030.290
visualizeClusters0.9040.1781.040
vsn0.4270.0110.437
wrapper.CVDistD_HC1.7300.7682.261
wrapper.compareNormalizationD_HC0.2160.0030.218
wrapper.corrMatrixD_HC0.2970.0120.305
wrapper.dapar.impute.mi000
wrapper.heatmapD0.0000.0000.001
wrapper.impute.KNN0.2080.0240.232
wrapper.impute.detQuant0.2790.0120.288
wrapper.impute.fixedValue0.2500.0110.261
wrapper.impute.mle0.2730.0150.288
wrapper.impute.pa0.2470.0080.254
wrapper.impute.pa20.2410.0030.243
wrapper.impute.slsa0.2350.0040.237
wrapper.mvImage0.1490.0030.151
wrapper.normalizeD0.2070.0000.206
wrapper.pca0.1430.0070.148
wrapperCalibrationPlot0.1330.0040.136
wrapperClassic1wayAnova1.5720.1031.628
wrapperRunClustering1.7940.2501.966
writeMSnsetToCSV0.0000.0000.001
writeMSnsetToExcel000