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This page was generated on 2025-10-10 12:05 -0400 (Fri, 10 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4854
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4642
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4587
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 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 1580/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PhyloProfile 2.1.11  (landing page)
Vinh Tran
Snapshot Date: 2025-10-09 13:45 -0400 (Thu, 09 Oct 2025)
git_url: https://git.bioconductor.org/packages/PhyloProfile
git_branch: devel
git_last_commit: 70712c9
git_last_commit_date: 2025-10-05 08:05:12 -0400 (Sun, 05 Oct 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 lconway

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: 2.1.11
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PhyloProfile.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PhyloProfile_2.1.11.tar.gz
StartedAt: 2025-10-10 00:08:21 -0400 (Fri, 10 Oct 2025)
EndedAt: 2025-10-10 00:12:04 -0400 (Fri, 10 Oct 2025)
EllapsedTime: 223.3 seconds
RetCode: 0
Status:   OK  
CheckDir: PhyloProfile.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PhyloProfile.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PhyloProfile_2.1.11.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/PhyloProfile.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PhyloProfile/DESCRIPTION’ ... OK
* this is package ‘PhyloProfile’ version ‘2.1.11’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 31 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 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 5.122  0.245   5.137
* 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:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL PhyloProfile
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘PhyloProfile’ ...
** this is package ‘PhyloProfile’ version ‘2.1.11’
** 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 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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 
  8.982   0.678   9.758 

Example timings

PhyloProfile.Rcheck/PhyloProfile-Ex.timings

nameusersystemelapsed
addDimRedTaxaColors0.9300.0400.979
addFeatureColors0.0340.0050.040
addRankDivisionPlot1.7890.0451.845
calcPresSpec0.0430.0020.045
checkColorPalette0.0000.0000.001
checkInputValidity0.0040.0010.006
checkNewick0.0030.0010.004
checkOmaID000
checkOverlapDomains0.0200.0010.022
clusterDataDend0.0230.0020.024
compareMedianTaxonGroups0.0270.0040.030
compareTaxonGroups0.0380.0040.042
createArchiPlot2.6270.0362.680
createDimRedPlotData0.7080.0240.734
createGeneAgePlot0.3800.0050.385
createLongMatrix0.0150.0080.023
createPercentageDistributionData0.0860.0150.102
createProfileFromOma0.0010.0010.001
createUnrootedTree0.0140.0020.015
createVarDistPlot0.3320.0040.338
createVariableDistributionData0.0070.0030.011
createVariableDistributionDataSubset0.0070.0020.009
dataCustomizedPlot0.0380.0030.040
dataFeatureTaxGroup0.0130.0020.015
dataMainPlot0.0430.0090.052
dataVarDistTaxGroup0.0060.0020.014
dimReduction0.7980.0130.814
estimateGeneAge0.1490.0140.163
fastaParser0.0390.0020.042
featureDistTaxPlot0.4330.0060.443
filterProfileData0.1430.0300.174
fromInputToProfile0.2000.0110.212
geneAgePlotDf0.0100.0010.009
generateSinglePlot0.5810.0070.591
getAllDomainsOma0.0000.0000.001
getAllFastaOma000
getCommonAncestor0.0370.0040.042
getCoreGene0.1150.0130.130
getDataClustering0.0190.0030.023
getDataForOneOma0.0010.0000.000
getDendrogram0.0610.0030.066
getDistanceMatrix0.0220.0020.023
getDomainFolder0.0010.0000.001
getFastaFromFasInput0.0180.0020.023
getFastaFromFile0.0140.0020.017
getFastaFromFolder0.0100.0020.012
getIDsRank0.0250.0040.029
getInputTaxaID0.0020.0010.004
getInputTaxaName0.0140.0040.018
getNameList0.0230.0360.058
getOmaDataForOneOrtholog000
getOmaDomainFromURL000
getOmaMembers000
getQualColForVector0.0000.0000.001
getSelectedFastaOma0.0010.0000.001
getSelectedTaxonNames0.0200.0050.026
getTaxHierarchy0.0170.0010.019
getTaxonomyInfo0.0160.0010.019
getTaxonomyMatrix0.1240.0910.240
getTaxonomyRanks0.0000.0000.001
gridArrangeSharedLegend000
groupLabelDimRedData0.0610.0070.069
heatmapPlotting0.5190.0050.525
heatmapPlottingFast5.1220.2455.137
highlightProfilePlot0.5760.0310.610
id2name0.0030.0010.004
joinPlotMergeLegends0.9740.0080.989
linearizeArchitecture0.0090.0000.010
mainTaxonomyRank000
modifyFeatureName0.0190.0160.035
pairDomainPlotting0.7220.0050.729
parseDomainInput0.0190.0150.035
parseInfoProfile0.1350.0100.145
plotDimRed1.4080.0191.434
plotDimRed3D1.0720.0571.142
prepareDimRedData0.0580.0070.066
processNcbiTaxonomy000
processOrthoID0.1330.0770.285
qualitativeColours0.0000.0000.001
rankIndexing0.0440.0010.046
reduceProfile0.0780.0030.081
resolveOverlapFeatures0.0190.0010.020
runPhyloProfile0.0930.0500.169
singleDomainPlotting0.3020.0040.307
sortDomains0.0100.0020.012
sortDomainsByList0.0110.0010.012
sortInputTaxa0.0320.0070.041
sortTaxaFromTree0.0150.0010.016
taxonomyTableCreator0.1830.0100.195
varDistTaxPlot1.3450.0151.370
wideToLong0.0130.0090.021
xmlParser0.0160.0020.019