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

This page was generated on 2025-09-03 12:04 -0400 (Wed, 03 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4826
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4616
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4563
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4541
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 1566/2321HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PhyloProfile 2.1.8  (landing page)
Vinh Tran
Snapshot Date: 2025-09-02 13:45 -0400 (Tue, 02 Sep 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 nebbiolo2

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.

raw results


Summary

Package: PhyloProfile
Version: 2.1.8
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:PhyloProfile.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings PhyloProfile_2.1.8.tar.gz
StartedAt: 2025-09-03 02:50:04 -0400 (Wed, 03 Sep 2025)
EndedAt: 2025-09-03 02:52:59 -0400 (Wed, 03 Sep 2025)
EllapsedTime: 175.1 seconds
RetCode: 0
Status:   OK  
CheckDir: PhyloProfile.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:PhyloProfile.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings PhyloProfile_2.1.8.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/PhyloProfile.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

PhyloProfile.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL PhyloProfile
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/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 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-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 
  6.332   0.390   6.712 

Example timings

PhyloProfile.Rcheck/PhyloProfile-Ex.timings

nameusersystemelapsed
addDimRedTaxaColors0.6370.0810.718
addFeatureColors0.0290.0100.039
addRankDivisionPlot0.6810.0970.777
calcPresSpec0.0470.0120.059
checkColorPalette0.0000.0000.001
checkInputValidity0.0020.0020.004
checkNewick0.0030.0000.003
checkOmaID000
checkOverlapDomains0.0140.0000.014
clusterDataDend0.0170.0000.017
compareMedianTaxonGroups0.0210.0020.023
compareTaxonGroups0.0280.0040.032
createArchiPlot2.6420.2642.906
createDimRedPlotData0.5800.0670.647
createGeneAgePlot0.2060.0070.213
createLongMatrix0.0130.0000.013
createPercentageDistributionData0.0650.0050.070
createProfileFromOma000
createUnrootedTree0.0110.0000.011
createVarDistPlot0.1470.0010.147
createVariableDistributionData0.0060.0000.006
createVariableDistributionDataSubset0.0070.0000.006
dataCustomizedPlot0.0310.0000.031
dataFeatureTaxGroup0.0120.0000.013
dataMainPlot0.0380.0000.038
dataVarDistTaxGroup0.0050.0000.005
dimReduction0.6010.2220.823
estimateGeneAge0.1200.0030.122
fastaParser0.0320.0010.034
featureDistTaxPlot0.1860.0060.193
filterProfileData0.0970.0090.106
fromInputToProfile0.1670.0080.175
geneAgePlotDf0.0090.0000.009
generateSinglePlot0.3820.0250.407
getAllDomainsOma0.0010.0000.001
getAllFastaOma000
getCommonAncestor0.0280.0060.034
getCoreGene0.1010.0070.108
getDataClustering0.0180.0000.018
getDataForOneOma000
getDendrogram0.0460.0070.053
getDistanceMatrix0.0160.0050.021
getDomainFolder0.0010.0000.001
getFastaFromFasInput0.0150.0010.016
getFastaFromFile0.010.000.01
getFastaFromFolder0.0080.0000.008
getIDsRank0.0220.0030.025
getInputTaxaID0.0010.0010.003
getInputTaxaName0.0120.0010.013
getNameList0.0150.0030.017
getOmaDataForOneOrtholog000
getOmaDomainFromURL000
getOmaMembers000
getQualColForVector0.0000.0000.001
getSelectedFastaOma000
getSelectedTaxonNames0.0130.0050.018
getTaxHierarchy0.0350.0060.042
getTaxonomyInfo0.0110.0060.017
getTaxonomyMatrix0.0690.0120.081
getTaxonomyRanks000
gridArrangeSharedLegend000
groupLabelDimRedData0.0530.0030.056
heatmapPlotting0.2780.0050.283
heatmapPlottingFast4.0790.6764.460
highlightProfilePlot0.3190.1490.468
id2name0.0050.0010.006
joinPlotMergeLegends0.5420.0900.632
linearizeArchitecture0.0080.0000.007
mainTaxonomyRank0.0010.0000.000
modifyFeatureName0.0090.0030.013
pairDomainPlotting0.4090.0030.412
parseDomainInput0.0090.0030.012
parseInfoProfile0.0980.0050.104
plotDimRed0.8770.0690.946
plotDimRed3D0.8430.0620.905
prepareDimRedData0.0490.0000.048
processNcbiTaxonomy000
processOrthoID0.1190.0180.171
qualitativeColours0.0000.0000.001
rankIndexing0.0410.0050.046
reduceProfile0.0650.0120.077
resolveOverlapFeatures0.0160.0000.016
runPhyloProfile000
singleDomainPlotting0.1760.0030.179
sortDomains0.0070.0000.007
sortDomainsByList0.0080.0000.007
sortInputTaxa0.0240.0010.025
sortTaxaFromTree0.0110.0000.011
taxonomyTableCreator0.0800.0040.084
varDistTaxPlot0.7560.0640.820
wideToLong0.0080.0000.009
xmlParser0.0120.0030.016