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This page was generated on 2025-10-21 12:06 -0400 (Tue, 21 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4887
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4677
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4622
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4642
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 1588/2353HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PhyloProfile 2.1.12  (landing page)
Vinh Tran
Snapshot Date: 2025-10-20 13:45 -0400 (Mon, 20 Oct 2025)
git_url: https://git.bioconductor.org/packages/PhyloProfile
git_branch: devel
git_last_commit: f3488bd
git_last_commit_date: 2025-10-10 13:16:29 -0400 (Fri, 10 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.6 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 kjohnson3

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: 2.1.12
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_2.1.12.tar.gz
StartedAt: 2025-10-20 21:19:09 -0400 (Mon, 20 Oct 2025)
EndedAt: 2025-10-20 21:20:17 -0400 (Mon, 20 Oct 2025)
EllapsedTime: 67.8 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_2.1.12.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/PhyloProfile.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PhyloProfile/DESCRIPTION’ ... OK
* this is package ‘PhyloProfile’ version ‘2.1.12’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 31 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-arm64/Resources/library’
* installing *source* package ‘PhyloProfile’ ...
** this is package ‘PhyloProfile’ version ‘2.1.12’
** 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 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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 
  2.902   0.176   3.081 

Example timings

PhyloProfile.Rcheck/PhyloProfile-Ex.timings

nameusersystemelapsed
addDimRedTaxaColors0.3110.0070.318
addFeatureColors0.0120.0010.013
addRankDivisionPlot0.3330.0090.342
calcPresSpec0.0120.0020.013
checkColorPalette0.0010.0000.000
checkInputValidity0.0010.0000.003
checkNewick0.0010.0010.001
checkOmaID0.0000.0000.001
checkOverlapDomains0.0050.0010.006
clusterDataDend0.2360.0020.239
compareMedianTaxonGroups0.0080.0010.009
compareTaxonGroups0.0100.0010.011
createArchiPlot0.6350.0130.652
createDimRedPlotData0.2350.0040.239
createGeneAgePlot0.0980.0010.099
createLongMatrix0.0050.0030.007
createPercentageDistributionData0.0230.0040.029
createProfileFromOma000
createUnrootedTree0.0040.0000.005
createVarDistPlot0.0840.0010.085
createVariableDistributionData0.0030.0020.004
createVariableDistributionDataSubset0.0030.0000.003
dataCustomizedPlot0.0110.0000.011
dataFeatureTaxGroup0.0050.0000.005
dataMainPlot0.0130.0030.016
dataVarDistTaxGroup0.0020.0000.002
dimReduction0.2510.0050.255
estimateGeneAge0.0430.0050.049
fastaParser0.0100.0010.011
featureDistTaxPlot0.1050.0010.107
filterProfileData0.0380.0080.047
fromInputToProfile0.0570.0040.061
geneAgePlotDf0.0030.0000.002
generateSinglePlot0.1440.0010.144
getAllDomainsOma000
getAllFastaOma000
getCommonAncestor0.0100.0020.011
getCoreGene0.0290.0050.034
getDataClustering0.0040.0000.006
getDataForOneOma000
getDendrogram0.0140.0010.015
getDistanceMatrix0.0050.0010.005
getDomainFolder000
getFastaFromFasInput0.0040.0010.004
getFastaFromFile0.0030.0000.003
getFastaFromFolder0.0020.0000.002
getIDsRank0.0050.0000.006
getInputTaxaID0.0010.0010.001
getInputTaxaName0.0040.0010.004
getNameList0.0070.0060.012
getOmaDataForOneOrtholog000
getOmaDomainFromURL000
getOmaMembers000
getQualColForVector000
getSelectedFastaOma000
getSelectedTaxonNames0.0050.0010.007
getTaxHierarchy0.0050.0010.005
getTaxonomyInfo0.0040.0010.004
getTaxonomyMatrix0.0370.0240.069
getTaxonomyRanks000
gridArrangeSharedLegend000
groupLabelDimRedData0.0180.0020.020
heatmapPlotting0.1260.0010.128
heatmapPlottingFast2.0070.0401.915
highlightProfilePlot0.1530.0090.162
id2name0.0020.0000.002
joinPlotMergeLegends0.2570.0020.260
linearizeArchitecture0.0030.0000.003
mainTaxonomyRank000
modifyFeatureName0.0060.0040.010
pairDomainPlotting0.1740.0010.178
parseDomainInput0.0060.0040.010
parseInfoProfile0.0350.0040.039
plotDimRed0.4060.0050.412
plotDimRed3D0.3280.0120.342
prepareDimRedData0.0170.0020.019
processNcbiTaxonomy000
processOrthoID0.0430.0190.075
qualitativeColours000
rankIndexing0.0140.0010.015
reduceProfile0.0230.0000.023
resolveOverlapFeatures0.0050.0000.005
runPhyloProfile0.0290.0140.043
singleDomainPlotting0.0790.0010.080
sortDomains0.0030.0010.003
sortDomainsByList0.0030.0000.003
sortInputTaxa0.0100.0030.012
sortTaxaFromTree0.0040.0000.004
taxonomyTableCreator0.0580.0040.061
varDistTaxPlot0.3420.0040.346
wideToLong0.0050.0010.006
xmlParser0.0060.0000.007