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This page was generated on 2021-08-02 15:04:45 -0400 (Mon, 02 Aug 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 1.24.7  (landing page)
Samuel Wieczorek
Snapshot Date: 2021-08-01 04:50:10 -0400 (Sun, 01 Aug 2021)
URL: https://git.bioconductor.org/packages/DAPAR
Branch: RELEASE_3_13
Last Commit: b1a45fc
Last Changed Date: 2021-07-29 23:25:03 -0400 (Thu, 29 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  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: 1.24.7
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_1.24.7.tar.gz
StartedAt: 2021-08-01 09:26:04 -0400 (Sun, 01 Aug 2021)
EndedAt: 2021-08-01 09:30:31 -0400 (Sun, 01 Aug 2021)
EllapsedTime: 266.8 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_1.24.7.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 ‘1.24.7’
* 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 ... 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 7.886  1.808   9.300
CVDistD_HC        3.984  1.710   5.205
* 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

##############################################################################
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###
### 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 
  8.393   0.545   8.914 

Example timings

DAPAR.Rcheck/DAPAR-Ex.timings

nameusersystemelapsed
AggregateMetacell7.8861.8089.300
BuildAdjacencyMatrix0.2620.0200.282
BuildColumnToProteinDataset1.0220.1201.102
BuildColumnToProteinDataset_par000
BuildMetaCell0.6530.0240.673
CVDistD_HC3.9841.7105.205
CountPep0.3220.0100.331
ExtendPalette0.0300.0050.033
GetCC1.6140.0941.703
GetColorsForConditions0.1990.0000.199
GetDetailedNbPeptides0.2220.0000.222
GetIndices_MetacellFiltering0.2280.0000.228
GetIndices_WholeLine0.2250.0020.227
GetIndices_WholeMatrix0.2240.0000.223
GetMatAdj0.2510.0180.268
Get_AllComparisons0.2060.0310.237
GlobalQuantileAlignment0.2440.0000.244
GraphPepProt0.2340.0000.234
LOESS0.930.010.94
MeanCentering0.2090.0030.211
MetaCellFiltering0.2580.0070.263
Metacell_generic0.5370.0110.542
Metacell_maxquant0.3910.0280.415
Metacell_proline000
NumericalFiltering0.2710.0070.277
NumericalgetIndicesOfLinesToRemove0.2090.0070.216
QuantileCentering0.2000.0030.203
SetCC2.4120.0672.471
SetMatAdj0.2560.0020.257
Set_POV_MEC_tags0.3410.0030.343
StringBasedFiltering0.2400.0120.250
StringBasedFiltering20.3830.0110.392
SumByColumns1.2710.0501.303
aggregateIter1.0310.1081.098
aggregateIterParallel0.0010.0000.000
aggregateMean0.9270.1501.033
aggregateSum0.8900.1080.962
aggregateTopn0.0000.0000.001
averageIntensities0.1920.0530.243
boxPlotD_HC0.3950.0650.448
buildGraph1.1320.0341.163
check.conditions0.2060.0000.207
check.design0.2070.0000.206
checkClusterability2.7560.7263.218
classic1wayAnova1.2150.0771.259
compareNormalizationD_HC2.2450.5982.664
compute_t_tests0.9380.0690.969
corrMatrixD_HC0.2870.0280.311
createMSnset1.7050.0931.785
dapar_hc_ExportMenu0.1200.0330.151
dapar_hc_chart0.0520.0040.054
deleteLinesFromIndices0.9140.0210.935
densityPlotD_HC1.9850.5852.399
diffAnaComputeFDR0.3710.0120.377
diffAnaGetSignificant0.2410.0200.257
diffAnaSave0.1870.0200.204
diffAnaVolcanoplot0.1870.0040.189
diffAnaVolcanoplot_rCharts0.0010.0000.001
display.CC.visNet1.1780.0281.199
enrich_GO0.0010.0000.000
findMECBlock0.2240.0030.226
formatLimmaResult0.1240.0040.126
formatPHResults3.3620.2953.550
get.pep.prot.cc4.2100.5494.746
getIndicesConditions0.2040.0000.205
getIndicesOfLinesToRemove0.2120.0020.214
getListNbValuesInLines0.1960.0030.200
getNumberOf0.2120.0030.215
getNumberOfEmptyLines0.2250.0040.228
getPourcentageOfMV0.2210.0000.220
getProcessingInfo0.1940.0020.196
getProteinsStats0.2370.0040.239
getQuantile4Imp0.2030.0000.202
getTextForAggregation0.0010.0000.001
getTextForAnaDiff0.0010.0000.001
getTextForGOAnalysis000
getTextForHypothesisTest0.0000.0010.000
getTextForNewDataset0.0000.0020.001
getTextForNormalization000
getTextForpeptideImputation000
getTextForproteinImputation000
group_GO0.0010.0000.000
hc_logFC_DensityPlot0.8210.2030.960
hc_mvTypePlot20.9090.1821.041
heatmapD0.0010.0000.001
heatmapForMissingValues0.1710.0040.174
histPValue_HC0.1780.0080.183
impute.pa20.2470.0030.247
limmaCompleteTest1.0310.0101.032
make.contrast0.20.00.2
make.design.10.1950.0030.198
make.design.20.0000.0000.001
make.design.30.2020.0000.203
make.design0.2060.0000.205
match.metacell0.2140.0050.219
metacellHisto_HC0.2490.0080.255
metacellPerLinesHistoPerCondition_HC0.3770.0190.393
metacellPerLinesHisto_HC0.2600.0200.278
metacombine000
mvImage1.6990.0791.757
my_hc_ExportMenu0.1570.0210.175
my_hc_chart0.1320.0280.156
nonzero0.0140.0040.017
plotJitter1.0870.0381.123
plotPCA_Eigen0.1940.0080.202
plotPCA_Eigen_hc0.1980.0030.202
plotPCA_Ind0.2010.0000.201
plotPCA_Var0.3050.0020.307
postHocTest3.0350.2323.170
proportionConRev_HC0.0380.0160.053
rbindMSnset0.2800.0040.281
reIntroduceMEC0.2970.0110.305
removeLines0.2290.0080.236
saveParameters0.1910.0080.199
search.metacell.tags0.0080.0000.008
test.design0.1950.0030.199
translatedRandomBeta0.0030.0080.011
violinPlotD0.2860.0040.288
visualizeClusters1.0070.1371.105
vsn0.4430.0110.453
wrapper.CVDistD_HC1.6670.7292.150
wrapper.compareNormalizationD_HC0.2100.0030.213
wrapper.corrMatrixD_HC0.3160.0150.328
wrapper.dapar.impute.mi0.0010.0000.000
wrapper.heatmapD000
wrapper.impute.KNN0.2390.0110.249
wrapper.impute.detQuant0.3540.0240.369
wrapper.impute.fixedValue0.2810.0080.287
wrapper.impute.mle0.2320.0160.246
wrapper.impute.pa0.2390.0190.257
wrapper.impute.pa20.2550.0000.252
wrapper.impute.slsa0.3660.0190.380
wrapper.mvImage0.1210.0040.123
wrapper.normalizeD0.2250.0000.224
wrapper.pca0.1160.0150.130
wrapperCalibrationPlot0.1260.0090.132
wrapperClassic1wayAnova1.5080.1281.587
wrapperRunClustering1.7390.2151.883
write.excel0.4320.0570.477
writeMSnsetToCSV0.0000.0000.001
writeMSnsetToExcel000