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This page was generated on 2025-04-02 19:32 -0400 (Wed, 02 Apr 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.3 (2025-02-28) -- "Trophy Case" 4764
palomino8Windows Server 2022 Datacenterx644.4.3 (2025-02-28 ucrt) -- "Trophy Case" 4495
merida1macOS 12.7.5 Montereyx86_644.4.3 (2025-02-28) -- "Trophy Case" 4522
kjohnson1macOS 13.6.6 Venturaarm644.4.3 (2025-02-28) -- "Trophy Case" 4449
taishanLinux (openEuler 24.03 LTS)aarch644.4.3 (2025-02-28) -- "Trophy Case" 4426
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

Package 1547/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PhyloProfile 1.20.4  (landing page)
Vinh Tran
Snapshot Date: 2025-03-31 13:00 -0400 (Mon, 31 Mar 2025)
git_url: https://git.bioconductor.org/packages/PhyloProfile
git_branch: RELEASE_3_20
git_last_commit: 44345df
git_last_commit_date: 2024-12-02 05:25:10 -0400 (Mon, 02 Dec 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for PhyloProfile on merida1

To the developers/maintainers of the PhyloProfile package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/PhyloProfile.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: PhyloProfile
Version: 1.20.4
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PhyloProfile.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PhyloProfile_1.20.4.tar.gz
StartedAt: 2025-04-01 07:09:04 -0400 (Tue, 01 Apr 2025)
EndedAt: 2025-04-01 07:15:49 -0400 (Tue, 01 Apr 2025)
EllapsedTime: 404.8 seconds
RetCode: 0
Status:   OK  
CheckDir: PhyloProfile.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PhyloProfile.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PhyloProfile_1.20.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/PhyloProfile.Rcheck’
* using R version 4.4.3 (2025-02-28)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PhyloProfile/DESCRIPTION’ ... OK
* this is package ‘PhyloProfile’ version ‘1.20.4’
* 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 ‘PhyloProfile’ 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 code 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
createArchiPlot     5.205  0.052   5.660
heatmapPlottingFast 4.718  0.306   5.086
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

PhyloProfile.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘PhyloProfile’ ...
** using staged installation
** R
** data
** 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 (PhyloProfile)

Tests output

PhyloProfile.Rcheck/tests/testthat.Rout


R version 4.4.3 (2025-02-28) -- "Trophy Case"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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(PhyloProfile)
> 
> test_check("PhyloProfile")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 20 ]
> 
> proc.time()
   user  system elapsed 
 16.158   1.050  19.491 

Example timings

PhyloProfile.Rcheck/PhyloProfile-Ex.timings

nameusersystemelapsed
addDimRedTaxaColors2.0270.1282.180
addFeatureColors0.0570.0040.063
addRankDivisionPlot1.6160.0401.672
calcPresSpec0.0980.0040.102
checkColorPalette0.0010.0010.001
checkInputValidity0.0080.0010.011
checkNewick0.0050.0020.006
checkOmaID000
checkOverlapDomains0.0300.0020.032
clusterDataDend0.0370.0030.042
compareMedianTaxonGroups0.0590.0070.070
compareTaxonGroups0.0740.0070.084
createArchiPlot5.2050.0525.660
createDimRedPlotData1.3110.0391.531
createGeneAgePlot0.4500.0040.508
createLongMatrix0.0320.0200.052
createPercentageDistributionData0.1950.0280.233
createProfileFromOma0.0000.0000.001
createUnrootedTree0.0340.0020.037
createVarDistPlot0.3670.0060.388
createVariableDistributionData0.0140.0110.025
createVariableDistributionDataSubset0.0140.0040.021
dataCustomizedPlot0.0400.0050.050
dataFeatureTaxGroup0.0280.0040.034
dataMainPlot0.0530.0220.083
dataVarDistTaxGroup0.0100.0040.015
dimReduction1.8810.0341.971
estimateGeneAge0.2760.0220.300
fastaParser0.0640.0040.070
featureDistTaxPlot0.4530.0070.469
filterProfileData0.2380.0800.320
fromInputToProfile0.2180.0310.251
geneAgePlotDf0.0150.0010.016
generateSinglePlot0.8370.0110.867
getAllDomainsOma000
getAllFastaOma000
getCommonAncestor0.1080.0110.126
getCoreGene0.1900.0180.224
getDataClustering0.0360.0040.041
getDataForOneOma0.0000.0000.001
getDendrogram0.1030.0040.113
getDistanceMatrix0.0350.0020.039
getDomainFolder0.0010.0000.001
getFastaFromFasInput0.0310.0020.033
getFastaFromFile0.0210.0020.024
getFastaFromFolder0.0150.0030.020
getIDsRank0.0450.0050.051
getInputTaxaID0.0040.0040.008
getInputTaxaName0.0230.0050.031
getNameList0.0430.0640.111
getOmaDataForOneOrtholog0.0010.0000.001
getOmaDomainFromURL0.0000.0000.001
getOmaMembers0.0000.0000.001
getQualColForVector0.0010.0000.001
getSelectedFastaOma0.0000.0000.001
getSelectedTaxonNames0.0360.0080.047
getTaxHierarchy0.0320.0030.037
getTaxonomyInfo0.0300.0030.035
getTaxonomyMatrix0.2330.2550.491
getTaxonomyRanks0.0000.0010.001
gridArrangeSharedLegend0.0010.0010.001
groupLabelDimRedData0.1000.0140.114
heatmapPlotting0.6340.0120.651
heatmapPlottingFast4.7180.3065.086
highlightProfilePlot0.6850.0140.787
id2name0.0080.0020.011
joinPlotMergeLegends1.3300.0471.571
linearizeArchitecture0.0190.0010.021
mainTaxonomyRank0.0000.0010.002
modifyFeatureName0.0370.0410.089
pairDomainPlotting1.0220.0091.191
parseDomainInput0.0350.0410.114
parseInfoProfile0.1650.0620.331
plotDimRed2.0080.0332.620
plotDimRed3D1.9150.0872.215
prepareDimRedData0.1010.0140.123
processNcbiTaxonomy0.0000.0010.001
processOrthoID0.2400.1120.444
qualitativeColours0.0010.0000.002
rankIndexing0.1190.0040.136
reduceProfile0.0290.0200.063
resolveOverlapFeatures0.0320.0020.037
runPhyloProfile000
singleDomainPlotting0.4410.0050.507
sortDomains0.0170.0020.023
sortDomainsByList0.0170.0020.021
sortInputTaxa0.0660.0100.087
sortTaxaFromTree0.0320.0020.040
taxonomyTableCreator0.2220.0100.267
varDistTaxPlot1.8580.0182.129
wideToLong0.0220.0200.045
xmlParser0.0320.0060.045