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This page was generated on 2025-10-11 12:04 -0400 (Sat, 11 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4864
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4652
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4597
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 1585/2346HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PhyloProfile 2.1.12  (landing page)
Vinh Tran
Snapshot Date: 2025-10-10 13:45 -0400 (Fri, 10 Oct 2025)
git_url: https://git.bioconductor.org/packages/PhyloProfile
git_branch: devel
git_last_commit: f3488bd
git_last_commit_date: 2025-10-10 13:16:29 -0400 (Fri, 10 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  YES
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  YES
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  YES
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: 2.1.12
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_2.1.12.tar.gz
StartedAt: 2025-10-11 00:06:38 -0400 (Sat, 11 Oct 2025)
EndedAt: 2025-10-11 00:10:06 -0400 (Sat, 11 Oct 2025)
EllapsedTime: 208.4 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_2.1.12.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 ‘2.1.12’
* 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 4.937  0.257   4.964
* 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 ‘2.1.12’
** 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 
  8.474   0.639   9.246 

Example timings

PhyloProfile.Rcheck/PhyloProfile-Ex.timings

nameusersystemelapsed
addDimRedTaxaColors0.8530.0400.902
addFeatureColors0.0320.0040.037
addRankDivisionPlot1.7080.0481.774
calcPresSpec0.0420.0020.045
checkColorPalette0.0000.0000.001
checkInputValidity0.0040.0010.006
checkNewick0.0020.0010.003
checkOmaID0.0000.0010.001
checkOverlapDomains0.0180.0010.019
clusterDataDend0.0190.0020.021
compareMedianTaxonGroups0.0210.0030.024
compareTaxonGroups0.0280.0030.033
createArchiPlot2.5140.0402.572
createDimRedPlotData0.7650.0250.794
createGeneAgePlot0.4240.0050.433
createLongMatrix0.0170.0090.026
createPercentageDistributionData0.0850.0160.101
createProfileFromOma000
createUnrootedTree0.0140.0020.015
createVarDistPlot0.3360.0050.343
createVariableDistributionData0.0070.0040.011
createVariableDistributionDataSubset0.0070.0020.009
dataCustomizedPlot0.0370.0030.040
dataFeatureTaxGroup0.0140.0020.016
dataMainPlot0.0430.0070.051
dataVarDistTaxGroup0.0050.0010.006
dimReduction0.7030.0130.720
estimateGeneAge0.1350.0140.150
fastaParser0.0370.0020.038
featureDistTaxPlot0.4030.0050.410
filterProfileData0.1330.0320.167
fromInputToProfile0.1850.0110.198
geneAgePlotDf0.0080.0000.008
generateSinglePlot0.5810.0070.590
getAllDomainsOma0.0000.0000.001
getAllFastaOma000
getCommonAncestor0.0310.0050.036
getCoreGene0.1150.0130.129
getDataClustering0.0180.0020.020
getDataForOneOma0.0000.0000.001
getDendrogram0.0510.0040.054
getDistanceMatrix0.0160.0010.018
getDomainFolder0.0010.0000.001
getFastaFromFasInput0.0160.0010.017
getFastaFromFile0.0140.0010.017
getFastaFromFolder0.0090.0020.011
getIDsRank0.0200.0020.023
getInputTaxaID0.0020.0020.004
getInputTaxaName0.0120.0040.016
getNameList0.0210.0250.047
getOmaDataForOneOrtholog000
getOmaDomainFromURL000
getOmaMembers000
getQualColForVector0.0000.0000.001
getSelectedFastaOma0.0000.0010.000
getSelectedTaxonNames0.0210.0060.027
getTaxHierarchy0.0160.0020.017
getTaxonomyInfo0.0180.0020.020
getTaxonomyMatrix0.1090.0870.199
getTaxonomyRanks0.0000.0000.001
gridArrangeSharedLegend000
groupLabelDimRedData0.0640.0070.071
heatmapPlotting0.5290.0060.538
heatmapPlottingFast4.9370.2574.964
highlightProfilePlot0.5880.0350.630
id2name0.0040.0010.005
joinPlotMergeLegends0.9040.0120.923
linearizeArchitecture0.0080.0010.009
mainTaxonomyRank0.0000.0010.001
modifyFeatureName0.0180.0320.051
pairDomainPlotting0.6390.0080.651
parseDomainInput0.0150.0220.037
parseInfoProfile0.1120.0080.122
plotDimRed1.3020.0211.331
plotDimRed3D1.1300.0821.230
prepareDimRedData0.0720.0130.086
processNcbiTaxonomy0.0000.0000.001
processOrthoID0.1530.1220.403
qualitativeColours0.0000.0000.001
rankIndexing0.0580.0020.060
reduceProfile0.0730.0040.079
resolveOverlapFeatures0.0210.0010.022
runPhyloProfile0.0960.0510.171
singleDomainPlotting0.3100.0040.316
sortDomains0.0090.0010.010
sortDomainsByList0.0090.0020.011
sortInputTaxa0.0290.0060.037
sortTaxaFromTree0.0110.0010.013
taxonomyTableCreator0.1480.0070.155
varDistTaxPlot1.2350.0131.260
wideToLong0.0130.0090.027
xmlParser0.0180.0040.022