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This page was generated on 2025-09-26 12:05 -0400 (Fri, 26 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4831
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4619
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4563
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4563
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 1576/2334HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PhyloProfile 2.1.8  (landing page)
Vinh Tran
Snapshot Date: 2025-09-25 13:45 -0400 (Thu, 25 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 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: 2.1.8
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_2.1.8.tar.gz
StartedAt: 2025-09-25 23:14:15 -0400 (Thu, 25 Sep 2025)
EndedAt: 2025-09-25 23:17:40 -0400 (Thu, 25 Sep 2025)
EllapsedTime: 204.8 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_2.1.8.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 ‘2.1.8’
* 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 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 5.04  0.231   5.048
* 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 ‘2.1.8’
** 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 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 
  8.351   0.631   9.085 

Example timings

PhyloProfile.Rcheck/PhyloProfile-Ex.timings

nameusersystemelapsed
addDimRedTaxaColors0.7570.0410.805
addFeatureColors0.0300.0040.035
addRankDivisionPlot1.2320.0331.273
calcPresSpec0.0500.0050.058
checkColorPalette0.0010.0010.001
checkInputValidity0.0050.0020.007
checkNewick0.0030.0010.004
checkOmaID000
checkOverlapDomains0.0230.0040.027
clusterDataDend0.0250.0040.029
compareMedianTaxonGroups0.0300.0050.036
compareTaxonGroups0.6100.0100.626
createArchiPlot2.5120.0442.580
createDimRedPlotData0.6890.0210.716
createGeneAgePlot0.3640.0040.371
createLongMatrix0.0160.0070.023
createPercentageDistributionData0.0790.0150.096
createProfileFromOma000
createUnrootedTree0.0140.0010.016
createVarDistPlot0.3210.0040.327
createVariableDistributionData0.0070.0030.011
createVariableDistributionDataSubset0.0080.0020.010
dataCustomizedPlot0.0370.0030.041
dataFeatureTaxGroup0.0160.0020.018
dataMainPlot0.0430.0090.057
dataVarDistTaxGroup0.0040.0020.008
dimReduction0.6910.0120.707
estimateGeneAge0.1280.0130.143
fastaParser0.0320.0020.035
featureDistTaxPlot0.3610.0040.368
filterProfileData0.1460.0290.177
fromInputToProfile0.1930.0110.205
geneAgePlotDf0.0090.0000.009
generateSinglePlot0.5970.0050.607
getAllDomainsOma000
getAllFastaOma000
getCommonAncestor0.0330.0040.038
getCoreGene0.1080.0110.120
getDataClustering0.0170.0020.019
getDataForOneOma000
getDendrogram0.0580.0030.064
getDistanceMatrix0.0200.0020.022
getDomainFolder0.0010.0010.001
getFastaFromFasInput0.0160.0010.017
getFastaFromFile0.0110.0010.012
getFastaFromFolder0.0070.0010.008
getIDsRank0.0230.0030.026
getInputTaxaID0.0030.0020.004
getInputTaxaName0.0130.0040.016
getNameList0.0190.0220.042
getOmaDataForOneOrtholog000
getOmaDomainFromURL000
getOmaMembers000
getQualColForVector0.0000.0010.000
getSelectedFastaOma000
getSelectedTaxonNames0.0190.0050.025
getTaxHierarchy0.0190.0030.022
getTaxonomyInfo0.0110.0020.013
getTaxonomyMatrix0.0970.0820.180
getTaxonomyRanks0.0010.0010.000
gridArrangeSharedLegend0.0000.0010.000
groupLabelDimRedData0.0560.0070.063
heatmapPlotting0.5130.0060.523
heatmapPlottingFast5.0400.2315.048
highlightProfilePlot0.5820.0280.615
id2name0.0040.0020.005
joinPlotMergeLegends1.0090.0111.028
linearizeArchitecture0.0120.0000.012
mainTaxonomyRank0.0000.0010.001
modifyFeatureName0.0190.0250.045
pairDomainPlotting0.7050.0050.715
parseDomainInput0.0160.0140.030
parseInfoProfile0.1280.0110.139
plotDimRed1.3730.0191.399
plotDimRed3D1.0460.0541.108
prepareDimRedData0.0660.0070.074
processNcbiTaxonomy0.0000.0010.001
processOrthoID0.1480.0870.320
qualitativeColours0.0000.0000.001
rankIndexing0.0510.0010.054
reduceProfile0.0710.0040.076
resolveOverlapFeatures0.0200.0010.021
runPhyloProfile000
singleDomainPlotting0.3080.0040.315
sortDomains0.0090.0010.011
sortDomainsByList0.0110.0010.012
sortInputTaxa0.0310.0060.038
sortTaxaFromTree0.0120.0010.013
taxonomyTableCreator0.0960.0050.105
varDistTaxPlot1.4050.0141.432
wideToLong0.0140.0070.020
xmlParser0.0190.0040.024