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This page was generated on 2025-10-16 11:41 -0400 (Thu, 16 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4833
merida1macOS 12.7.6 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4614
kjohnson1macOS 13.7.5 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4555
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4586
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: 2025-10-13 13:40 -0400 (Mon, 13 Oct 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 12.7.6 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.7.5 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: 2025-10-14 12:32:08 -0000 (Tue, 14 Oct 2025)
EndedAt: 2025-10-14 12:35:56 -0000 (Tue, 14 Oct 2025)
EllapsedTime: 228.2 seconds
RetCode: 0
Status:   OK  
CheckDir: PhyloProfile.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### 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
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
heatmapPlottingFast 5.834  0.185    5.87
* 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 
 10.185   1.035  11.249 

Example timings

PhyloProfile.Rcheck/PhyloProfile-Ex.timings

nameusersystemelapsed
addDimRedTaxaColors0.9450.2151.168
addFeatureColors0.0370.0160.054
addRankDivisionPlot1.5570.3911.952
calcPresSpec0.0420.0080.051
checkColorPalette0.0010.0000.001
checkInputValidity0.0050.0000.007
checkNewick0.0030.0000.003
checkOmaID0.0010.0000.000
checkOverlapDomains0.0210.0000.021
clusterDataDend0.0190.0080.027
compareMedianTaxonGroups0.0270.0080.034
compareTaxonGroups0.6880.2400.930
createArchiPlot3.2690.0833.360
createDimRedPlotData0.8300.0320.864
createGeneAgePlot0.5080.0200.529
createLongMatrix0.0160.0000.016
createPercentageDistributionData0.0890.0030.094
createProfileFromOma000
createUnrootedTree0.0170.0000.018
createVarDistPlot0.4010.0110.414
createVariableDistributionData0.0070.0010.007
createVariableDistributionDataSubset0.0050.0030.008
dataCustomizedPlot0.0400.0040.044
dataFeatureTaxGroup0.0180.0010.018
dataMainPlot0.0490.0070.056
dataVarDistTaxGroup0.0050.0010.006
dimReduction0.8270.0230.852
estimateGeneAge0.1540.0120.167
fastaParser0.0390.0040.044
featureDistTaxPlot0.470.000.47
filterProfileData0.1520.0070.160
fromInputToProfile0.2350.0000.235
geneAgePlotDf0.0090.0000.010
generateSinglePlot0.7370.0040.742
getAllDomainsOma0.0010.0000.000
getAllFastaOma000
getCommonAncestor0.0430.0000.043
getCoreGene0.1170.0000.117
getDataClustering0.0210.0000.021
getDataForOneOma000
getDendrogram0.0610.0000.061
getDistanceMatrix0.020.000.02
getDomainFolder0.0010.0000.001
getFastaFromFasInput0.0170.0000.017
getFastaFromFile0.0120.0000.013
getFastaFromFolder0.0090.0000.010
getIDsRank0.0250.0000.027
getInputTaxaID0.0020.0000.003
getInputTaxaName0.0130.0000.013
getNameList0.0140.0040.018
getOmaDataForOneOrtholog000
getOmaDomainFromURL000
getOmaMembers000
getQualColForVector000
getSelectedFastaOma0.0000.0000.001
getSelectedTaxonNames0.020.000.02
getTaxHierarchy0.0180.0000.019
getTaxonomyInfo0.0170.0000.017
getTaxonomyMatrix0.0720.0280.099
getTaxonomyRanks000
gridArrangeSharedLegend000
groupLabelDimRedData0.0680.0040.073
heatmapPlotting0.6950.0150.712
heatmapPlottingFast5.8340.1855.870
highlightProfilePlot0.7470.0360.784
id2name0.0030.0030.005
joinPlotMergeLegends1.2810.0031.290
linearizeArchitecture0.0120.0000.012
mainTaxonomyRank0.0010.0000.001
modifyFeatureName0.0120.0040.016
pairDomainPlotting0.8740.0280.904
parseDomainInput0.0110.0040.015
parseInfoProfile0.1600.0040.168
plotDimRed1.6360.1031.745
plotDimRed3D1.2630.0401.306
prepareDimRedData0.0650.0040.069
processNcbiTaxonomy000
processOrthoID0.1430.0330.275
qualitativeColours000
rankIndexing0.0740.0000.074
reduceProfile0.0960.0120.108
resolveOverlapFeatures0.0230.0000.023
runPhyloProfile000
singleDomainPlotting0.4170.0360.454
sortDomains0.0060.0040.010
sortDomainsByList0.0120.0000.012
sortInputTaxa0.0410.0000.041
sortTaxaFromTree0.0170.0000.017
taxonomyTableCreator0.1260.0080.135
varDistTaxPlot1.8130.3362.152
wideToLong0.0090.0030.013
xmlParser0.0250.0010.025