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This page was generated on 2022-06-22 11:04:52 -0400 (Wed, 22 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics" 4331
palomino4Windows Server 2022 Datacenterx644.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics" 4136
lconwaymacOS 12.2.1 Montereyx86_644.2.0 Patched (2022-05-29 r82424) -- "Vigorous Calisthenics" 4147
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? 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 463/2118HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DAPAR 1.29.0  (landing page)
Samuel Wieczorek
Snapshot Date: 2022-06-21 14:00:02 -0400 (Tue, 21 Jun 2022)
git_url: https://git.bioconductor.org/packages/DAPAR
git_branch: master
git_last_commit: 3be0327
git_last_commit_date: 2022-06-17 01:41:45 -0400 (Fri, 17 Jun 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.2.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: DAPAR
Version: 1.29.0
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:DAPAR.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/library --no-vignettes --timings DAPAR_1.29.0.tar.gz
StartedAt: 2022-06-21 19:31:01 -0400 (Tue, 21 Jun 2022)
EndedAt: 2022-06-21 19:35:13 -0400 (Tue, 21 Jun 2022)
EllapsedTime: 252.9 seconds
RetCode: 0
Status:   OK  
CheckDir: DAPAR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:DAPAR.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/library --no-vignettes --timings DAPAR_1.29.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/DAPAR.Rcheck’
* using R version 4.2.0 Patched (2022-06-02 r82447)
* 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 ‘1.29.0’
* 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 ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘igraph’
A package should be listed in only one of these fields.
* 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
'library' or 'require' calls in package code:
  ‘doParallel’ ‘foreach’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespaces in Imports field not imported from:
  ‘Cairo’ ‘DAPARdata’ ‘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'
BuildColumnToProteinDataset_par: no visible global function definition
  for ‘%dopar%’
BuildColumnToProteinDataset_par: no visible global function definition
  for ‘foreach’
GetIndices_MetacellFiltering: no visible global function definition for
  ‘tsop’
aggregateIterParallel: no visible global function definition for
  ‘%dopar%’
aggregateIterParallel: no visible global function definition for
  ‘foreach’
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’
createMSnset: no visible global function definition for
  ‘package.version’
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’
finalizeAggregation: no visible global function definition for
  ‘package.version’
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’
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<-’
pepa.test: no visible binding for global variable ‘de’
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’
wrapperRunClustering: no visible global function definition for
  ‘ExpressionSet’
Undefined global functions or variables:
  %dopar% A B Condition ExpressionSet FDR_threshold P.Value Pr(>F)1
  adjusted_pvalues bitr cond condition de desc enrichGO feature foreach
  g input intensity last layout_nicely nodes<- package.version post_hoc
  str_c textGOParams tsop x y
Consider adding
  importFrom("utils", "de")
to your NAMESPACE file.
* 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 6.403  0.163   6.567
get.pep.prot.cc   5.001  0.687   5.651
* 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
  ‘/home/biocbuild/bbs-3.16-bioc/meat/DAPAR.Rcheck/00check.log’
for details.



Installation output

DAPAR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL DAPAR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-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 4.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics"
Copyright (C) 2022 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 
  8.683   0.497   9.173 

Example timings

DAPAR.Rcheck/DAPAR-Ex.timings

nameusersystemelapsed
AggregateMetacell6.4030.1636.567
BuildAdjacencyMatrix0.2850.0080.293
BuildColumnToProteinDataset0.8360.0680.904
BuildColumnToProteinDataset_par0.0010.0000.000
BuildMetaCell0.5070.0230.531
CVDistD_HC2.0610.0372.104
CountPep0.2870.0120.299
ExtendPalette0.0240.0000.023
GetCC2.2530.0602.313
GetColorsForConditions0.2250.0040.228
GetDetailedNbPeptides0.3350.0040.338
GetIndices_MetacellFiltering0.2480.0000.248
GetIndices_WholeLine0.2460.0000.245
GetIndices_WholeMatrix0.2540.0000.254
GetMatAdj0.3190.0040.323
Get_AllComparisons0.1950.0000.196
GlobalQuantileAlignment0.2750.0000.275
GraphPepProt0.2580.0000.258
LOESS0.9520.0040.955
MeanCentering0.2560.0040.260
MetaCellFiltering0.2700.0120.282
Metacell_generic0.4290.0000.429
Metacell_maxquant0.4130.0000.413
Metacell_proline0.0010.0000.000
NumericalFiltering0.2930.0040.297
NumericalgetIndicesOfLinesToRemove0.2620.0000.262
QuantileCentering0.2570.0000.257
SetCC1.6240.0521.676
SetMatAdj0.3110.0080.318
Set_POV_MEC_tags0.2580.0040.261
StringBasedFiltering0.2690.0080.276
StringBasedFiltering20.2720.0040.277
SumByColumns1.0200.0081.028
aggregateIter0.8260.0000.826
aggregateIterParallel000
aggregateMean0.7920.0000.793
aggregateSum1.4660.0241.490
aggregateTopn000
averageIntensities0.4940.0360.524
boxPlotD_HC0.3120.0680.369
buildGraph1.1180.0531.161
check.conditions0.2420.0000.241
check.design0.2340.0040.238
checkClusterability2.5550.9993.239
classic1wayAnova1.0780.1911.232
compareNormalizationD_HC2.5680.7383.080
compute_t_tests0.8170.1350.915
corrMatrixD_HC0.3520.0200.368
createMSnset1.6640.1171.765
dapar_hc_ExportMenu0.1140.0330.145
dapar_hc_chart0.0490.0120.060
deleteLinesFromIndices0.4220.0570.477
densityPlotD_HC2.6030.8223.199
diffAnaComputeFDR0.3720.0540.414
diffAnaGetSignificant0.2610.0200.273
diffAnaSave0.3000.0290.319
diffAnaVolcanoplot0.1690.0040.168
diffAnaVolcanoplot_rCharts0.0010.0000.000
display.CC.visNet1.8210.1621.967
enrich_GO000
findMECBlock0.2650.0030.267
formatLimmaResult0.1180.0130.128
formatPHResults2.7390.4603.082
get.pep.prot.cc5.0010.6875.651
getIndicesConditions0.2310.0040.235
getIndicesOfLinesToRemove0.2600.0000.258
getListNbValuesInLines0.2380.0040.241
getNumberOf0.2470.0110.257
getNumberOfEmptyLines0.2590.0040.263
getPourcentageOfMV0.2580.0040.261
getProcessingInfo0.2400.0040.243
getProteinsStats0.2810.0080.288
getQuantile4Imp0.2480.0040.252
getTextForAggregation000
getTextForAnaDiff000
getTextForGOAnalysis0.0010.0000.000
getTextForHypothesisTest0.0000.0000.001
getTextForNewDataset0.0020.0000.002
getTextForNormalization0.0010.0000.000
getTextForpeptideImputation0.0000.0000.001
getTextForproteinImputation000
group_GO000
hc_logFC_DensityPlot1.1160.3001.326
hc_mvTypePlot21.0300.3551.309
heatmapD000
heatmapForMissingValues0.2060.0120.214
histPValue_HC0.1810.0290.203
impute.pa20.2970.0240.317
limmaCompleteTest1.0800.0711.140
make.contrast0.240.000.24
make.design.10.2410.0000.240
make.design.2000
make.design.30.2460.0000.246
make.design0.2370.0000.237
match.metacell0.2610.0030.262
metacellHisto_HC0.2910.0110.300
metacellPerLinesHistoPerCondition_HC0.4040.0160.416
metacellPerLinesHisto_HC0.2890.0240.311
metacombine000
mvImage1.8420.0771.896
my_hc_ExportMenu0.1270.0480.173
my_hc_chart0.1120.0200.130
nonzero0.0150.0000.014
plotJitter1.1890.0641.246
plotPCA_Eigen0.2410.0000.241
plotPCA_Eigen_hc0.2360.0030.239
plotPCA_Ind0.2360.0040.240
plotPCA_Var0.2340.0000.234
postHocTest2.7640.3072.965
proportionConRev_HC0.0420.0160.056
rbindMSnset0.3440.0320.370
reIntroduceMEC0.3390.0110.345
removeLines0.2850.0040.286
saveParameters0.2420.0000.242
search.metacell.tags0.0080.0000.007
test.design0.2360.0000.236
translatedRandomBeta0.0030.0000.003
violinPlotD0.2680.0150.281
visualizeClusters1.0320.1161.101
vsn0.4500.0030.452
wrapper.CVDistD_HC1.8450.8202.406
wrapper.compareNormalizationD_HC0.2640.0000.263
wrapper.corrMatrixD_HC0.3550.0280.378
wrapper.dapar.impute.mi000
wrapper.heatmapD0.0000.0000.001
wrapper.impute.KNN0.2890.0100.296
wrapper.impute.detQuant0.4190.0250.433
wrapper.impute.fixedValue0.3400.0120.347
wrapper.impute.mle0.3050.0000.302
wrapper.impute.pa0.3450.0070.349
wrapper.impute.pa20.3030.0080.306
wrapper.impute.slsa0.4060.0160.417
wrapper.mvImage0.1260.0090.132
wrapper.normalizeD0.2650.0000.264
wrapper.pca0.1230.0120.131
wrapperCalibrationPlot0.1450.0200.160
wrapperClassic1wayAnova1.5860.1781.710
wrapperRunClustering2.1190.2112.236
write.excel0.5710.0990.649
writeMSnsetToCSV000
writeMSnsetToExcel000