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This page was generated on 2025-09-04 12:05 -0400 (Thu, 04 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4822
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4617
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4564
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4541
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 1566/2321HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PhyloProfile 2.1.8  (landing page)
Vinh Tran
Snapshot Date: 2025-09-03 13:45 -0400 (Wed, 03 Sep 2025)
git_url: https://git.bioconductor.org/packages/PhyloProfile
git_branch: devel
git_last_commit: d12ba8b
git_last_commit_date: 2025-06-23 14:44:32 -0400 (Mon, 23 Jun 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 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 lconway

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: 2.1.8
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_2.1.8.tar.gz
StartedAt: 2025-09-03 22:51:47 -0400 (Wed, 03 Sep 2025)
EndedAt: 2025-09-03 22:54:57 -0400 (Wed, 03 Sep 2025)
EllapsedTime: 190.8 seconds
RetCode: 0
Status:   OK  
CheckDir: PhyloProfile.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### 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_2.1.8.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/PhyloProfile.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* 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 ‘2.1.8’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 32 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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
* 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/4.5-x86_64/Resources/library’
* installing *source* package ‘PhyloProfile’ ...
** this is package ‘PhyloProfile’ version ‘2.1.8’
** 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 4.5.1 (2025-06-13) -- "Great Square Root"
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 22 ]
> 
> proc.time()
   user  system elapsed 
  7.695   0.574   8.320 

Example timings

PhyloProfile.Rcheck/PhyloProfile-Ex.timings

nameusersystemelapsed
addDimRedTaxaColors0.8470.0430.899
addFeatureColors0.0370.0050.043
addRankDivisionPlot0.9500.0380.992
calcPresSpec0.0440.0030.046
checkColorPalette0.0010.0000.001
checkInputValidity0.0050.0010.006
checkNewick0.0020.0010.003
checkOmaID000
checkOverlapDomains0.0200.0010.021
clusterDataDend0.0240.0020.025
compareMedianTaxonGroups0.0280.0020.031
compareTaxonGroups0.0380.0050.044
createArchiPlot3.0820.0373.132
createDimRedPlotData0.7460.0200.768
createGeneAgePlot0.2490.0030.253
createLongMatrix0.0150.0080.023
createPercentageDistributionData0.0850.0150.101
createProfileFromOma000
createUnrootedTree0.0130.0010.014
createVarDistPlot0.1810.0040.187
createVariableDistributionData0.0090.0040.013
createVariableDistributionDataSubset0.0080.0020.010
dataCustomizedPlot0.0380.0020.040
dataFeatureTaxGroup0.0180.0020.021
dataMainPlot0.0530.0080.062
dataVarDistTaxGroup0.0050.0020.008
dimReduction0.7550.0110.768
estimateGeneAge0.1550.0140.169
fastaParser0.0390.0020.041
featureDistTaxPlot0.2320.0040.236
filterProfileData0.1540.0350.189
fromInputToProfile0.2000.0110.212
geneAgePlotDf0.0090.0000.010
generateSinglePlot0.4440.0050.452
getAllDomainsOma0.0000.0000.001
getAllFastaOma000
getCommonAncestor0.0330.0050.039
getCoreGene0.1180.0120.131
getDataClustering0.0180.0020.020
getDataForOneOma000
getDendrogram0.0490.0030.053
getDistanceMatrix0.0170.0020.019
getDomainFolder0.0010.0000.001
getFastaFromFasInput0.0190.0020.021
getFastaFromFile0.0130.0020.015
getFastaFromFolder0.0090.0020.012
getIDsRank0.0240.0030.027
getInputTaxaID0.0020.0010.004
getInputTaxaName0.0150.0030.018
getNameList0.0240.0220.046
getOmaDataForOneOrtholog000
getOmaDomainFromURL000
getOmaMembers0.0000.0010.000
getQualColForVector000
getSelectedFastaOma0.0000.0000.001
getSelectedTaxonNames0.0390.0050.044
getTaxHierarchy0.0160.0010.017
getTaxonomyInfo0.0130.0010.016
getTaxonomyMatrix0.0920.0860.179
getTaxonomyRanks0.0000.0010.001
gridArrangeSharedLegend0.0000.0010.000
groupLabelDimRedData0.0620.0060.068
heatmapPlotting0.3290.0030.334
heatmapPlottingFast4.1350.2074.100
highlightProfilePlot0.3570.0100.370
id2name0.0050.0010.007
joinPlotMergeLegends0.6480.0360.688
linearizeArchitecture0.0090.0000.009
mainTaxonomyRank0.0000.0000.001
modifyFeatureName0.0150.0200.035
pairDomainPlotting0.4790.0040.486
parseDomainInput0.0180.0120.031
parseInfoProfile0.1320.0110.145
plotDimRed1.0510.0171.073
plotDimRed3D1.0550.0561.119
prepareDimRedData0.0620.0070.070
processNcbiTaxonomy000
processOrthoID0.1440.0780.308
qualitativeColours0.0010.0000.001
rankIndexing0.0560.0020.058
reduceProfile0.0790.0030.084
resolveOverlapFeatures0.0210.0010.023
runPhyloProfile000
singleDomainPlotting0.2450.0040.253
sortDomains0.0090.0010.010
sortDomainsByList0.0110.0010.012
sortInputTaxa0.0360.0080.044
sortTaxaFromTree0.0140.0020.016
taxonomyTableCreator0.1150.0050.122
varDistTaxPlot1.0630.0111.085
wideToLong0.0160.0090.026
xmlParser0.0210.0040.026