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This page was generated on 2025-10-18 12:07 -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 taishan

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: PhyloProfile
Version: 2.1.12
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:PhyloProfile.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings PhyloProfile_2.1.12.tar.gz
StartedAt: 2025-10-17 12:11:01 -0000 (Fri, 17 Oct 2025)
EndedAt: 2025-10-17 12:14:47 -0000 (Fri, 17 Oct 2025)
EllapsedTime: 226.3 seconds
RetCode: 0
Status:   OK  
CheckDir: PhyloProfile.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:PhyloProfile.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings PhyloProfile_2.1.12.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/PhyloProfile.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* 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 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 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:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL PhyloProfile
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0/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 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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 
  9.906   0.468  10.620 

Example timings

PhyloProfile.Rcheck/PhyloProfile-Ex.timings

nameusersystemelapsed
addDimRedTaxaColors0.9190.0400.963
addFeatureColors0.0400.0040.046
addRankDivisionPlot2.0240.1122.141
calcPresSpec0.0390.0040.042
checkColorPalette0.0000.0000.001
checkInputValidity0.0050.0000.005
checkNewick0.0030.0000.002
checkOmaID000
checkOverlapDomains0.0190.0000.018
clusterDataDend0.0230.0000.022
compareMedianTaxonGroups0.0300.0000.029
compareTaxonGroups0.040.000.04
createArchiPlot3.2310.0443.283
createDimRedPlotData0.7740.0240.800
createGeneAgePlot0.4920.0000.493
createLongMatrix0.0160.0000.016
createPercentageDistributionData0.0900.0040.094
createProfileFromOma000
createUnrootedTree0.0170.0000.017
createVarDistPlot0.4040.0120.418
createVariableDistributionData0.0070.0000.008
createVariableDistributionDataSubset0.0090.0000.009
dataCustomizedPlot0.0450.0000.046
dataFeatureTaxGroup0.0180.0000.018
dataMainPlot0.0450.0080.053
dataVarDistTaxGroup0.0070.0000.007
dimReduction0.7740.0320.809
estimateGeneAge0.1700.0040.174
fastaParser0.0460.0000.047
featureDistTaxPlot0.4980.0040.503
filterProfileData0.1630.0080.171
fromInputToProfile0.2410.0000.243
geneAgePlotDf0.010.000.01
generateSinglePlot0.6890.0070.698
getAllDomainsOma000
getAllFastaOma000
getCommonAncestor0.0420.0000.042
getCoreGene0.1190.0030.124
getDataClustering0.0210.0010.022
getDataForOneOma0.0000.0000.001
getDendrogram0.0580.0030.061
getDistanceMatrix0.0180.0040.021
getDomainFolder0.0010.0000.001
getFastaFromFasInput0.0130.0040.018
getFastaFromFile0.0120.0000.013
getFastaFromFolder0.0100.0000.011
getIDsRank0.0270.0000.027
getInputTaxaID0.0020.0000.003
getInputTaxaName0.0120.0000.013
getNameList0.0180.0000.018
getOmaDataForOneOrtholog000
getOmaDomainFromURL000
getOmaMembers0.0010.0000.000
getQualColForVector0.0000.0000.001
getSelectedFastaOma0.0000.0000.001
getSelectedTaxonNames0.0190.0000.020
getTaxHierarchy0.020.000.02
getTaxonomyInfo0.0190.0000.018
getTaxonomyMatrix0.0930.0070.101
getTaxonomyRanks000
gridArrangeSharedLegend000
groupLabelDimRedData0.0890.0000.092
heatmapPlotting0.6240.0000.625
heatmapPlottingFast4.6730.1844.745
highlightProfilePlot0.7270.0040.733
id2name0.0050.0000.005
joinPlotMergeLegends1.2610.0001.264
linearizeArchitecture0.0110.0000.012
mainTaxonomyRank000
modifyFeatureName0.0110.0040.015
pairDomainPlotting0.9020.0280.932
parseDomainInput0.0100.0040.014
parseInfoProfile0.1490.0030.154
plotDimRed1.6330.0051.642
plotDimRed3D1.1870.0191.210
prepareDimRedData0.0780.0000.079
processNcbiTaxonomy000
processOrthoID0.1520.0380.330
qualitativeColours0.0010.0000.000
rankIndexing0.0620.0000.062
reduceProfile0.1190.0040.123
resolveOverlapFeatures0.0210.0000.020
runPhyloProfile0.0950.0150.110
singleDomainPlotting0.3760.0040.380
sortDomains0.0090.0000.009
sortDomainsByList0.0110.0000.011
sortInputTaxa0.0350.0000.035
sortTaxaFromTree0.0150.0000.015
taxonomyTableCreator0.1340.0000.136
varDistTaxPlot1.6070.0001.612
wideToLong0.0060.0040.011
xmlParser0.0170.0040.022