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This page was generated on 2022-06-22 11:07:23 -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 lconway


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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DAPAR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DAPAR_1.29.0.tar.gz
StartedAt: 2022-06-21 19:47:32 -0400 (Tue, 21 Jun 2022)
EndedAt: 2022-06-21 19:52:27 -0400 (Tue, 21 Jun 2022)
EllapsedTime: 295.0 seconds
RetCode: 0
Status:   OK  
CheckDir: DAPAR.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DAPAR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DAPAR_1.29.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/DAPAR.Rcheck’
* using R version 4.2.0 Patched (2022-05-29 r82424)
* 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 ‘1.29.0’
* 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 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        6.764  0.101   6.892
get.pep.prot.cc          4.788  0.966   5.771
checkClusterability      3.388  2.111   5.487
compareNormalizationD_HC 3.709  1.646   5.397
densityPlotD_HC          3.665  1.574   5.239
* 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-3.16-bioc/meat/DAPAR.Rcheck/00check.log’
for details.



Installation output

DAPAR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL DAPAR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/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 4.2.0 Patched (2022-05-29 r82424) -- "Vigorous Calisthenics"
Copyright (C) 2022 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 
  9.195   0.473   9.695 

Example timings

DAPAR.Rcheck/DAPAR-Ex.timings

nameusersystemelapsed
AggregateMetacell6.7640.1016.892
BuildAdjacencyMatrix0.2700.0030.274
BuildColumnToProteinDataset0.9510.0160.972
BuildColumnToProteinDataset_par0.0000.0010.000
BuildMetaCell0.6210.0350.661
CVDistD_HC2.1110.1362.268
CountPep0.3670.0100.381
ExtendPalette0.0270.0010.029
GetCC2.2610.0632.335
GetColorsForConditions0.2390.0030.242
GetDetailedNbPeptides0.3880.0120.401
GetIndices_MetacellFiltering0.2840.0040.289
GetIndices_WholeLine0.2850.0040.289
GetIndices_WholeMatrix0.2690.0050.274
GetMatAdj0.3550.0180.375
Get_AllComparisons0.1920.0050.198
GlobalQuantileAlignment0.2900.0040.295
GraphPepProt0.2910.0050.298
LOESS0.9100.0180.931
MeanCentering0.2740.0090.284
MetaCellFiltering0.2860.0030.290
Metacell_generic0.5400.0130.556
Metacell_maxquant0.5550.0210.582
Metacell_proline0.0000.0010.001
NumericalFiltering0.2620.0050.267
NumericalgetIndicesOfLinesToRemove0.3030.0030.308
QuantileCentering0.2930.0030.297
SetCC1.6380.0451.688
SetMatAdj0.3520.0080.360
Set_POV_MEC_tags0.3190.0040.326
StringBasedFiltering0.3160.0040.322
StringBasedFiltering20.2890.0040.295
SumByColumns1.0880.0201.111
aggregateIter0.8640.0050.870
aggregateIterParallel000
aggregateMean0.9160.0070.926
aggregateSum1.5820.0271.616
aggregateTopn000
averageIntensities0.4700.0990.585
boxPlotD_HC0.4380.2000.643
buildGraph1.2140.0841.303
check.conditions0.2820.0060.292
check.design0.2620.0050.267
checkClusterability3.3882.1115.487
classic1wayAnova1.2330.2431.486
compareNormalizationD_HC3.7091.6465.397
compute_t_tests1.0570.2751.341
corrMatrixD_HC0.4020.0770.481
createMSnset2.0670.1612.240
dapar_hc_ExportMenu0.1570.1500.310
dapar_hc_chart0.0620.0520.116
deleteLinesFromIndices0.4730.0370.513
densityPlotD_HC3.6651.5745.239
diffAnaComputeFDR0.4570.1170.579
diffAnaGetSignificant0.2830.0640.349
diffAnaSave0.3040.0600.367
diffAnaVolcanoplot0.1590.0300.190
diffAnaVolcanoplot_rCharts0.0000.0010.001
display.CC.visNet1.7820.1341.923
enrich_GO000
findMECBlock0.2810.0130.296
formatLimmaResult0.1460.0280.175
formatPHResults3.4270.7354.194
get.pep.prot.cc4.7880.9665.771
getIndicesConditions0.2610.0040.266
getIndicesOfLinesToRemove0.2570.0100.268
getListNbValuesInLines0.2320.0030.235
getNumberOf0.2840.0290.318
getNumberOfEmptyLines0.2920.0090.305
getPourcentageOfMV0.2580.0110.269
getProcessingInfo0.2510.0040.256
getProteinsStats0.3060.0120.320
getQuantile4Imp0.2600.0040.267
getTextForAggregation0.0010.0000.001
getTextForAnaDiff0.0010.0000.000
getTextForGOAnalysis0.0010.0010.001
getTextForHypothesisTest000
getTextForNewDataset0.0020.0000.003
getTextForNormalization0.0010.0000.000
getTextForpeptideImputation0.0010.0010.001
getTextForproteinImputation000
group_GO0.0000.0010.000
hc_logFC_DensityPlot1.3320.6511.991
hc_mvTypePlot21.5940.6842.297
heatmapD000
heatmapForMissingValues0.1740.0270.201
histPValue_HC0.2040.0760.282
impute.pa20.3290.0340.366
limmaCompleteTest1.2420.0861.339
make.contrast0.2530.0040.259
make.design.10.2560.0040.259
make.design.20.0000.0000.001
make.design.30.2830.0040.288
make.design0.2780.0040.284
match.metacell0.3110.0150.329
metacellHisto_HC0.3470.0600.411
metacellPerLinesHistoPerCondition_HC0.4920.1190.623
metacellPerLinesHisto_HC0.3400.0640.406
metacombine0.0000.0010.001
mvImage2.1040.1992.307
my_hc_ExportMenu0.1460.1490.311
my_hc_chart0.1500.1510.306
nonzero0.0200.0010.021
plotJitter1.1880.1101.303
plotPCA_Eigen0.2640.0030.268
plotPCA_Eigen_hc0.2140.0030.216
plotPCA_Ind0.2810.0050.287
plotPCA_Var0.2760.0040.282
postHocTest3.4790.7514.247
proportionConRev_HC0.0610.0700.133
rbindMSnset0.3550.0340.391
reIntroduceMEC0.4230.0390.464
removeLines0.3340.0240.358
saveParameters0.2960.0060.305
search.metacell.tags0.0080.0020.010
test.design0.2910.0040.297
translatedRandomBeta0.0030.0070.009
violinPlotD0.2750.0270.306
visualizeClusters1.2420.3011.550
vsn0.5540.0160.573
wrapper.CVDistD_HC2.6411.7894.402
wrapper.compareNormalizationD_HC0.2690.0040.274
wrapper.corrMatrixD_HC0.3900.0710.463
wrapper.dapar.impute.mi000
wrapper.heatmapD000
wrapper.impute.KNN0.3350.0200.357
wrapper.impute.detQuant0.5180.0740.594
wrapper.impute.fixedValue0.3830.0380.421
wrapper.impute.mle0.3420.0210.365
wrapper.impute.pa0.3580.0220.380
wrapper.impute.pa20.3290.0270.356
wrapper.impute.slsa0.4350.0370.470
wrapper.mvImage0.1410.0280.170
wrapper.normalizeD0.2830.0040.287
wrapper.pca0.1350.0230.158
wrapperCalibrationPlot0.1550.0260.182
wrapperClassic1wayAnova1.7920.3342.122
wrapperRunClustering2.4060.5862.998
write.excel0.6840.1460.837
writeMSnsetToCSV000
writeMSnsetToExcel0.0000.0000.001