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This page was generated on 2025-08-04 12:12 -0400 (Mon, 04 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4796
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4536
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4578
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4519
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4517
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 1561/2313HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PhyloProfile 2.1.8  (landing page)
Vinh Tran
Snapshot Date: 2025-08-03 13:25 -0400 (Sun, 03 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 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    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 13.7.1 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: 2025-08-01 09:36:08 -0000 (Fri, 01 Aug 2025)
EndedAt: 2025-08-01 09:40:31 -0000 (Fri, 01 Aug 2025)
EllapsedTime: 262.5 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
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
createArchiPlot 3.498  0.021   6.078
* 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 
  8.458   0.366   9.666 

Example timings

PhyloProfile.Rcheck/PhyloProfile-Ex.timings

nameusersystemelapsed
addDimRedTaxaColors0.8360.0241.065
addFeatureColors0.0370.0040.084
addRankDivisionPlot1.0530.0751.573
calcPresSpec0.0430.0000.084
checkColorPalette0.0010.0000.001
checkInputValidity0.0050.0010.015
checkNewick0.0030.0000.007
checkOmaID000
checkOverlapDomains0.0180.0000.034
clusterDataDend0.0230.0000.048
compareMedianTaxonGroups0.0310.0000.043
compareTaxonGroups0.0410.0000.043
createArchiPlot3.4980.0216.078
createDimRedPlotData0.7380.0300.806
createGeneAgePlot0.3020.0040.335
createLongMatrix0.0160.0000.015
createPercentageDistributionData0.0900.0000.127
createProfileFromOma000
createUnrootedTree0.0160.0000.024
createVarDistPlot0.2020.0000.203
createVariableDistributionData0.0070.0000.007
createVariableDistributionDataSubset0.0080.0000.008
dataCustomizedPlot0.0410.0000.040
dataFeatureTaxGroup0.0160.0000.016
dataMainPlot0.0470.0000.047
dataVarDistTaxGroup0.0060.0000.006
dimReduction0.7390.0080.748
estimateGeneAge0.1540.0000.154
fastaParser0.0380.0040.079
featureDistTaxPlot0.2490.0040.279
filterProfileData0.1200.0110.131
fromInputToProfile0.2220.0120.235
geneAgePlotDf0.0100.0000.011
generateSinglePlot0.5210.0310.567
getAllDomainsOma000
getAllFastaOma000
getCommonAncestor0.0440.0020.046
getCoreGene0.1140.0040.119
getDataClustering0.0190.0040.023
getDataForOneOma000
getDendrogram0.0610.0000.061
getDistanceMatrix0.0210.0000.021
getDomainFolder0.0010.0000.001
getFastaFromFasInput0.0180.0000.017
getFastaFromFile0.0130.0000.020
getFastaFromFolder0.0050.0040.020
getIDsRank0.0270.0000.047
getInputTaxaID0.0030.0000.002
getInputTaxaName0.0130.0000.012
getNameList0.0140.0040.018
getOmaDataForOneOrtholog0.0010.0000.000
getOmaDomainFromURL000
getOmaMembers000
getQualColForVector0.0000.0000.001
getSelectedFastaOma000
getSelectedTaxonNames0.0140.0050.019
getTaxHierarchy0.0380.0000.038
getTaxonomyInfo0.0170.0000.017
getTaxonomyMatrix0.0820.0150.098
getTaxonomyRanks0.0010.0000.000
gridArrangeSharedLegend0.0000.0000.001
groupLabelDimRedData0.0570.0080.089
heatmapPlotting0.3720.0000.376
heatmapPlottingFast3.6980.0884.114
highlightProfilePlot0.4580.0000.460
id2name0.0050.0000.005
joinPlotMergeLegends0.8280.0240.891
linearizeArchitecture0.0120.0000.012
mainTaxonomyRank0.0010.0000.001
modifyFeatureName0.0120.0030.016
pairDomainPlotting0.6380.0040.656
parseDomainInput0.0110.0040.014
parseInfoProfile0.1360.0080.144
plotDimRed1.2110.0031.536
plotDimRed3D1.1070.0121.326
prepareDimRedData0.0640.0000.064
processNcbiTaxonomy000
processOrthoID0.1760.0180.579
qualitativeColours0.0000.0000.001
rankIndexing0.0660.0040.143
reduceProfile0.0850.0120.199
resolveOverlapFeatures0.0220.0000.042
runPhyloProfile000
singleDomainPlotting0.2990.0080.485
sortDomains0.010.000.01
sortDomainsByList0.0120.0000.012
sortInputTaxa0.0320.0080.040
sortTaxaFromTree0.0160.0000.016
taxonomyTableCreator0.1290.0080.206
varDistTaxPlot1.1660.0081.228
wideToLong0.0110.0000.011
xmlParser0.0220.0000.039