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This page was generated on 2025-10-18 12:04 -0400 (Sat, 18 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" 4632
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: 2025-10-17 13:45 -0400 (Fri, 17 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 nebbiolo2

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: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:PhyloProfile.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings PhyloProfile_2.1.12.tar.gz
StartedAt: 2025-10-18 03:12:09 -0400 (Sat, 18 Oct 2025)
EndedAt: 2025-10-18 03:15:10 -0400 (Sat, 18 Oct 2025)
EllapsedTime: 181.2 seconds
RetCode: 0
Status:   OK  
CheckDir: PhyloProfile.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:PhyloProfile.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings PhyloProfile_2.1.12.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/PhyloProfile.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* 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 loading without being on the library search path ... 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

PhyloProfile.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL PhyloProfile
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-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 (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 
  7.259   0.362   7.615 

Example timings

PhyloProfile.Rcheck/PhyloProfile-Ex.timings

nameusersystemelapsed
addDimRedTaxaColors0.7100.0490.761
addFeatureColors0.0250.0060.030
addRankDivisionPlot1.4030.0641.468
calcPresSpec0.0310.0110.041
checkColorPalette0.0010.0010.001
checkInputValidity0.0040.0000.005
checkNewick0.0020.0000.002
checkOmaID000
checkOverlapDomains0.0140.0010.015
clusterDataDend0.0170.0000.018
compareMedianTaxonGroups0.0200.0060.024
compareTaxonGroups0.0290.0040.033
createArchiPlot2.0050.0432.050
createDimRedPlotData0.5430.0350.579
createGeneAgePlot0.2930.0030.296
createLongMatrix0.0110.0010.012
createPercentageDistributionData0.0630.0000.064
createProfileFromOma000
createUnrootedTree0.0110.0000.011
createVarDistPlot0.2490.0010.250
createVariableDistributionData0.0060.0000.006
createVariableDistributionDataSubset0.0070.0000.006
dataCustomizedPlot0.0300.0010.030
dataFeatureTaxGroup0.0120.0020.012
dataMainPlot0.0330.0000.035
dataVarDistTaxGroup0.0040.0000.005
dimReduction0.5810.0100.592
estimateGeneAge0.1180.0010.118
fastaParser0.0310.0000.031
featureDistTaxPlot0.3050.0010.306
filterProfileData0.1270.0040.130
fromInputToProfile0.1550.0030.157
geneAgePlotDf0.0080.0000.007
generateSinglePlot0.4740.0300.503
getAllDomainsOma000
getAllFastaOma000
getCommonAncestor0.0270.0000.027
getCoreGene0.0820.0010.084
getDataClustering0.0140.0000.014
getDataForOneOma000
getDendrogram0.0430.0000.042
getDistanceMatrix0.0140.0010.014
getDomainFolder0.0010.0000.000
getFastaFromFasInput0.0130.0000.013
getFastaFromFile0.0090.0000.008
getFastaFromFolder0.0060.0000.006
getIDsRank0.0140.0030.017
getInputTaxaID0.0020.0000.002
getInputTaxaName0.0090.0010.010
getNameList0.0120.0020.014
getOmaDataForOneOrtholog000
getOmaDomainFromURL000
getOmaMembers000
getQualColForVector000
getSelectedFastaOma000
getSelectedTaxonNames0.0130.0010.015
getTaxHierarchy0.0120.0010.013
getTaxonomyInfo0.0110.0010.012
getTaxonomyMatrix0.0670.0080.075
getTaxonomyRanks000
gridArrangeSharedLegend000
groupLabelDimRedData0.0570.0010.058
heatmapPlotting0.3990.0000.399
heatmapPlottingFast4.2720.3574.342
highlightProfilePlot0.4630.0250.488
id2name0.0030.0010.004
joinPlotMergeLegends0.7510.0000.751
linearizeArchitecture0.0070.0000.007
mainTaxonomyRank0.0000.0000.001
modifyFeatureName0.0090.0030.012
pairDomainPlotting0.5330.0010.533
parseDomainInput0.0100.0020.012
parseInfoProfile0.0920.0000.092
plotDimRed1.0480.0041.052
plotDimRed3D0.7950.0090.803
prepareDimRedData0.0440.0010.045
processNcbiTaxonomy000
processOrthoID0.1040.0190.134
qualitativeColours000
rankIndexing0.0380.0000.039
reduceProfile0.0830.0000.083
resolveOverlapFeatures0.0120.0020.013
runPhyloProfile0.0770.0100.087
singleDomainPlotting0.2380.0000.240
sortDomains0.0050.0000.006
sortDomainsByList0.0070.0010.007
sortInputTaxa0.0250.0000.025
sortTaxaFromTree0.010.000.01
taxonomyTableCreator0.090.000.09
varDistTaxPlot1.0390.0121.052
wideToLong0.0090.0010.009
xmlParser0.0130.0030.016