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This page was generated on 2025-08-21 11:42 -0400 (Thu, 21 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4604
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4545
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4579
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 1577/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PhyloProfile 2.0.6  (landing page)
Vinh Tran
Snapshot Date: 2025-08-18 13:40 -0400 (Mon, 18 Aug 2025)
git_url: https://git.bioconductor.org/packages/PhyloProfile
git_branch: RELEASE_3_21
git_last_commit: a0b5fbc
git_last_commit_date: 2025-06-23 15:02:10 -0400 (Mon, 23 Jun 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for PhyloProfile on kunpeng2

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: 2.0.6
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_2.0.6.tar.gz
StartedAt: 2025-08-19 12:26:41 -0000 (Tue, 19 Aug 2025)
EndedAt: 2025-08-19 12:30:09 -0000 (Tue, 19 Aug 2025)
EllapsedTime: 208.1 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_2.0.6.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/PhyloProfile.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* 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-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PhyloProfile/DESCRIPTION’ ... OK
* this is package ‘PhyloProfile’ version ‘2.0.6’
* 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-devel_2025-02-19/site-library’
* installing *source* package ‘PhyloProfile’ ...
** this is package ‘PhyloProfile’ version ‘2.0.6’
** 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 Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
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 
  8.777   0.363   9.149 

Example timings

PhyloProfile.Rcheck/PhyloProfile-Ex.timings

nameusersystemelapsed
addDimRedTaxaColors0.9040.0280.938
addFeatureColors0.0370.0040.043
addRankDivisionPlot1.0100.0441.055
calcPresSpec0.0440.0000.045
checkColorPalette0.0010.0000.000
checkInputValidity0.0060.0000.006
checkNewick0.0030.0000.003
checkOmaID000
checkOverlapDomains0.020.000.02
clusterDataDend0.0230.0000.024
compareMedianTaxonGroups0.0310.0000.032
compareTaxonGroups0.0420.0000.042
createArchiPlot3.5660.0563.627
createDimRedPlotData0.8230.0480.872
createGeneAgePlot0.2840.0040.289
createLongMatrix0.0160.0000.015
createPercentageDistributionData0.0850.0040.089
createProfileFromOma000
createUnrootedTree0.0170.0000.018
createVarDistPlot0.2050.0000.206
createVariableDistributionData0.0070.0000.007
createVariableDistributionDataSubset0.0080.0000.008
dataCustomizedPlot0.0370.0040.041
dataFeatureTaxGroup0.0120.0040.016
dataMainPlot0.0450.0040.049
dataVarDistTaxGroup0.0060.0000.007
dimReduction0.8020.0200.823
estimateGeneAge0.1560.0040.161
fastaParser0.0410.0000.041
featureDistTaxPlot0.270.000.27
filterProfileData0.1240.0160.140
fromInputToProfile0.2150.0080.223
geneAgePlotDf0.010.000.01
generateSinglePlot0.5430.0000.545
getAllDomainsOma000
getAllFastaOma000
getCommonAncestor0.0460.0000.045
getCoreGene0.1190.0000.118
getDataClustering0.0210.0000.021
getDataForOneOma000
getDendrogram0.0600.0000.061
getDistanceMatrix0.0210.0000.021
getDomainFolder0.0000.0000.001
getFastaFromFasInput0.0170.0000.017
getFastaFromFile0.0090.0040.013
getFastaFromFolder0.0090.0000.010
getIDsRank0.0270.0000.027
getInputTaxaID0.0030.0000.002
getInputTaxaName0.0140.0000.014
getNameList0.0150.0040.019
getOmaDataForOneOrtholog000
getOmaDomainFromURL000
getOmaMembers000
getQualColForVector000
getSelectedFastaOma000
getSelectedTaxonNames0.0380.0000.037
getTaxHierarchy0.0190.0000.019
getTaxonomyInfo0.0170.0000.018
getTaxonomyMatrix0.0830.0200.104
getTaxonomyRanks000
gridArrangeSharedLegend000
groupLabelDimRedData0.0640.0000.064
heatmapPlotting0.3740.0000.375
heatmapPlottingFast4.7240.1394.716
highlightProfilePlot0.4530.0000.455
id2name0.0050.0000.005
joinPlotMergeLegends0.8480.0000.850
linearizeArchitecture0.0100.0000.011
mainTaxonomyRank000
modifyFeatureName0.0120.0040.016
pairDomainPlotting0.6230.0000.625
parseDomainInput0.0110.0040.015
parseInfoProfile0.1480.0040.153
plotDimRed1.2870.0001.290
plotDimRed3D1.2100.0161.229
prepareDimRedData0.0610.0200.081
processNcbiTaxonomy000
processOrthoID0.1410.0430.304
qualitativeColours0.0000.0000.001
rankIndexing0.0930.0040.098
reduceProfile0.0700.0000.069
resolveOverlapFeatures0.0180.0040.022
runPhyloProfile000
singleDomainPlotting0.2980.0040.303
sortDomains0.0100.0000.011
sortDomainsByList0.0140.0000.013
sortInputTaxa0.0330.0120.045
sortTaxaFromTree0.0190.0000.018
taxonomyTableCreator0.1300.0000.131
varDistTaxPlot1.2210.0041.228
wideToLong0.0110.0000.011
xmlParser0.0170.0040.021