Back to Multiple platform build/check report for BioC 3.16
ABC[D]EFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2022-06-22 11:06:00 -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 palomino4


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: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DAPAR.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings DAPAR_1.29.0.tar.gz
StartedAt: 2022-06-22 00:52:23 -0400 (Wed, 22 Jun 2022)
EndedAt: 2022-06-22 00:56:52 -0400 (Wed, 22 Jun 2022)
EllapsedTime: 268.6 seconds
RetCode: 0
Status:   OK  
CheckDir: DAPAR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DAPAR.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings DAPAR_1.29.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/DAPAR.Rcheck'
* using R version 4.2.0 Patched (2022-06-02 r82447 ucrt)
* using platform: x86_64-w64-mingw32 (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 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 6.24   0.06    6.32
get.pep.prot.cc   4.52   0.66    5.19
* 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
  'F:/biocbuild/bbs-3.16-bioc/meat/DAPAR.Rcheck/00check.log'
for details.



Installation output

DAPAR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.16/bioc/src/contrib/DAPAR_1.29.0.tar.gz && rm -rf DAPAR.buildbin-libdir && mkdir DAPAR.buildbin-libdir && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DAPAR.buildbin-libdir DAPAR_1.29.0.tar.gz && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL DAPAR_1.29.0.zip && rm DAPAR_1.29.0.tar.gz DAPAR_1.29.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  8 3119k    8  263k    0     0  2889k      0  0:00:01 --:--:--  0:00:01 2898k
100 3119k  100 3119k    0     0  9063k      0 --:--:-- --:--:-- --:--:-- 9068k
only one architecture so ignoring '--merge-multiarch'
* 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
* MD5 sums
packaged installation of 'DAPAR' as DAPAR_1.29.0.zip
* DONE (DAPAR)
* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library'
package 'DAPAR' successfully unpacked and MD5 sums checked

Tests output

DAPAR.Rcheck/tests/testthat.Rout


R version 4.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 
   8.85    0.75    9.67 

Example timings

DAPAR.Rcheck/DAPAR-Ex.timings

nameusersystemelapsed
AggregateMetacell6.240.066.32
BuildAdjacencyMatrix0.230.000.24
BuildColumnToProteinDataset0.880.040.92
BuildColumnToProteinDataset_par000
BuildMetaCell0.700.031.02
CVDistD_HC2.560.234.73
CountPep0.380.020.59
ExtendPalette0.030.000.03
GetCC2.190.012.21
GetColorsForConditions0.20.00.2
GetDetailedNbPeptides0.390.000.39
GetIndices_MetacellFiltering0.220.000.22
GetIndices_WholeLine0.220.000.21
GetIndices_WholeMatrix0.250.000.25
GetMatAdj0.830.000.83
Get_AllComparisons0.210.000.24
GlobalQuantileAlignment0.270.000.26
GraphPepProt0.220.000.22
LOESS0.860.030.89
MeanCentering0.220.000.22
MetaCellFiltering0.280.000.28
Metacell_generic0.580.050.63
Metacell_maxquant0.570.000.58
Metacell_proline000
NumericalFiltering0.290.000.28
NumericalgetIndicesOfLinesToRemove0.250.000.25
QuantileCentering0.230.000.23
SetCC1.800.011.81
SetMatAdj0.250.020.27
Set_POV_MEC_tags0.230.000.23
StringBasedFiltering0.250.000.25
StringBasedFiltering20.240.010.25
SumByColumns1.120.021.14
aggregateIter0.910.000.91
aggregateIterParallel000
aggregateMean0.780.020.79
aggregateSum1.640.061.71
aggregateTopn000
averageIntensities0.450.070.51
boxPlotD_HC0.330.250.58
buildGraph1.550.011.56
check.conditions0.220.000.22
check.design0.20.00.2
checkClusterability1.830.111.94
classic1wayAnova1.140.091.24
compareNormalizationD_HC2.170.272.43
compute_t_tests0.840.020.86
corrMatrixD_HC0.360.100.47
createMSnset1.920.001.92
dapar_hc_ExportMenu0.240.240.49
dapar_hc_chart0.080.050.14
deleteLinesFromIndices0.230.010.25
densityPlotD_HC2.300.282.58
diffAnaComputeFDR0.400.070.48
diffAnaGetSignificant0.230.000.23
diffAnaSave0.190.000.19
diffAnaVolcanoplot0.140.010.15
diffAnaVolcanoplot_rCharts000
display.CC.visNet1.280.051.63
enrich_GO000
findMECBlock0.320.020.32
formatLimmaResult0.150.030.19
formatPHResults2.670.112.80
get.pep.prot.cc4.520.665.19
getIndicesConditions0.180.000.19
getIndicesOfLinesToRemove0.210.000.20
getListNbValuesInLines0.180.000.19
getNumberOf0.210.000.21
getNumberOfEmptyLines0.220.000.22
getPourcentageOfMV0.250.000.25
getProcessingInfo0.180.000.18
getProteinsStats0.240.000.24
getQuantile4Imp0.170.020.19
getTextForAggregation000
getTextForAnaDiff000
getTextForGOAnalysis000
getTextForHypothesisTest000
getTextForNewDataset000
getTextForNormalization000
getTextForpeptideImputation000
getTextForproteinImputation000
group_GO000
hc_logFC_DensityPlot0.810.191.02
hc_mvTypePlot20.850.251.11
heatmapD000
heatmapForMissingValues0.130.020.14
histPValue_HC0.140.120.26
impute.pa20.220.020.24
limmaCompleteTest0.890.030.92
make.contrast0.190.000.18
make.design.10.170.010.19
make.design.20.000.020.02
make.design.30.170.030.20
make.design0.190.020.20
match.metacell0.200.010.22
metacellHisto_HC0.230.080.35
metacellPerLinesHistoPerCondition_HC0.430.200.64
metacellPerLinesHisto_HC0.230.130.40
metacombine000
mvImage1.560.111.67
my_hc_ExportMenu0.140.250.44
my_hc_chart0.180.200.39
nonzero0.010.000.02
plotJitter1.140.001.14
plotPCA_Eigen0.200.000.21
plotPCA_Eigen_hc0.190.000.18
plotPCA_Ind0.210.000.21
plotPCA_Var0.180.000.19
postHocTest2.640.082.71
proportionConRev_HC0.030.120.16
rbindMSnset0.270.000.27
reIntroduceMEC0.270.000.26
removeLines0.250.000.25
saveParameters0.20.00.2
search.metacell.tags0.010.000.02
test.design0.190.000.19
translatedRandomBeta0.020.000.01
violinPlotD0.200.020.24
visualizeClusters0.920.010.94
vsn0.50.00.5
wrapper.CVDistD_HC1.220.151.38
wrapper.compareNormalizationD_HC0.250.010.26
wrapper.corrMatrixD_HC0.260.130.41
wrapper.dapar.impute.mi000
wrapper.heatmapD000
wrapper.impute.KNN0.220.000.22
wrapper.impute.detQuant0.330.000.32
wrapper.impute.fixedValue0.270.000.27
wrapper.impute.mle0.230.000.23
wrapper.impute.pa0.220.010.24
wrapper.impute.pa20.200.020.22
wrapper.impute.slsa0.330.030.36
wrapper.mvImage0.140.000.14
wrapper.normalizeD0.20.00.2
wrapper.pca0.100.000.09
wrapperCalibrationPlot0.120.000.13
wrapperClassic1wayAnova1.470.081.55
wrapperRunClustering1.920.102.02
write.excel0.520.040.64
writeMSnsetToCSV000
writeMSnsetToExcel000