Back to Multiple platform build/check report for BioC 3.22:   simplified   long
ABCDEFGHIJKLMNO[P]QRSTUVWXYZ

This page was generated on 2025-08-22 12:07 -0400 (Fri, 22 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4821
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4599
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4541
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4539
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 1565/2319HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PhyloProfile 2.1.8  (landing page)
Vinh Tran
Snapshot Date: 2025-08-21 13:45 -0400 (Thu, 21 Aug 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 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: 2.1.8
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_2.1.8.tar.gz
StartedAt: 2025-08-22 11:00:50 -0000 (Fri, 22 Aug 2025)
EndedAt: 2025-08-22 11:04:09 -0000 (Fri, 22 Aug 2025)
EllapsedTime: 199.3 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_2.1.8.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 ‘2.1.8’
* 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 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 ‘2.1.8’
** 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 4.5.0 (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 
  8.688   0.590   9.289 

Example timings

PhyloProfile.Rcheck/PhyloProfile-Ex.timings

nameusersystemelapsed
addDimRedTaxaColors0.8570.0200.886
addFeatureColors0.0430.0040.049
addRankDivisionPlot1.1190.0721.196
calcPresSpec0.0490.0040.053
checkColorPalette0.0010.0000.001
checkInputValidity0.0060.0000.007
checkNewick0.0030.0000.003
checkOmaID000
checkOverlapDomains0.0200.0020.022
clusterDataDend0.0280.0000.029
compareMedianTaxonGroups0.0320.0000.033
compareTaxonGroups0.0470.0000.048
createArchiPlot3.6560.0883.755
createDimRedPlotData0.7450.0280.775
createGeneAgePlot0.2980.0040.303
createLongMatrix0.0040.0120.016
createPercentageDistributionData0.0850.0040.090
createProfileFromOma000
createUnrootedTree0.0160.0000.016
createVarDistPlot0.2270.0000.227
createVariableDistributionData0.0070.0000.007
createVariableDistributionDataSubset0.0090.0000.010
dataCustomizedPlot0.0460.0000.046
dataFeatureTaxGroup0.0180.0000.018
dataMainPlot0.0490.0040.053
dataVarDistTaxGroup0.0070.0000.006
dimReduction0.7270.0360.764
estimateGeneAge0.1570.0240.182
fastaParser0.0490.0000.049
featureDistTaxPlot0.2900.0080.299
filterProfileData0.1480.0080.157
fromInputToProfile0.2380.0240.262
geneAgePlotDf0.0110.0000.011
generateSinglePlot0.5770.0000.579
getAllDomainsOma000
getAllFastaOma0.0000.0000.001
getCommonAncestor0.0370.0040.041
getCoreGene0.1220.0040.126
getDataClustering0.0220.0000.023
getDataForOneOma000
getDendrogram0.0610.0000.062
getDistanceMatrix0.0210.0000.021
getDomainFolder0.0010.0000.000
getFastaFromFasInput0.0170.0000.018
getFastaFromFile0.0120.0000.014
getFastaFromFolder0.0090.0000.010
getIDsRank0.0270.0000.028
getInputTaxaID0.0020.0000.003
getInputTaxaName0.0120.0000.012
getNameList0.0130.0030.017
getOmaDataForOneOrtholog000
getOmaDomainFromURL0.0000.0000.001
getOmaMembers000
getQualColForVector000
getSelectedFastaOma000
getSelectedTaxonNames0.020.000.02
getTaxHierarchy0.040.000.04
getTaxonomyInfo0.0180.0000.018
getTaxonomyMatrix0.0900.0080.099
getTaxonomyRanks000
gridArrangeSharedLegend0.0000.0000.001
groupLabelDimRedData0.0690.0000.070
heatmapPlotting0.3900.0080.398
heatmapPlottingFast3.5910.1283.590
highlightProfilePlot0.4290.0080.437
id2name0.0040.0000.005
joinPlotMergeLegends0.7970.0040.803
linearizeArchitecture0.0110.0000.011
mainTaxonomyRank0.0010.0000.000
modifyFeatureName0.0110.0040.015
pairDomainPlotting0.6150.0000.617
parseDomainInput0.0140.0000.014
parseInfoProfile0.1360.0040.140
plotDimRed1.1760.0281.208
plotDimRed3D1.1480.0321.182
prepareDimRedData0.0560.0120.069
processNcbiTaxonomy000
processOrthoID0.1490.0260.303
qualitativeColours0.0000.0000.001
rankIndexing0.0610.0040.066
reduceProfile0.0830.0080.091
resolveOverlapFeatures0.0210.0000.020
runPhyloProfile000
singleDomainPlotting0.2750.0040.279
sortDomains0.0080.0000.009
sortDomainsByList0.0110.0000.010
sortInputTaxa0.0390.0040.043
sortTaxaFromTree0.0160.0000.016
taxonomyTableCreator0.1220.0000.124
varDistTaxPlot1.2350.0201.259
wideToLong0.0120.0000.012
xmlParser0.0230.0000.024