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This page was generated on 2025-08-21 11:41 -0400 (Thu, 21 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4604
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4545
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4579
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: 2025-08-18 13:40 -0400 (Mon, 18 Aug 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 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 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 kjohnson1

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: 2.0.6
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_2.0.6.tar.gz
StartedAt: 2025-08-20 07:05:18 -0400 (Wed, 20 Aug 2025)
EndedAt: 2025-08-20 07:08:24 -0400 (Wed, 20 Aug 2025)
EllapsedTime: 186.1 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_2.0.6.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/PhyloProfile.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.5
* 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 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 4.858  0.213   4.875
* 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-arm64/Resources/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 version 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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 
  7.723   0.614   8.435 

Example timings

PhyloProfile.Rcheck/PhyloProfile-Ex.timings

nameusersystemelapsed
addDimRedTaxaColors0.8350.0460.895
addFeatureColors0.0350.0030.038
addRankDivisionPlot0.6210.0350.657
calcPresSpec0.0270.0020.030
checkColorPalette0.0010.0000.001
checkInputValidity0.0020.0000.003
checkNewick0.0020.0000.002
checkOmaID000
checkOverlapDomains0.0090.0010.011
clusterDataDend0.0180.0020.020
compareMedianTaxonGroups0.0250.0030.028
compareTaxonGroups0.0280.0020.030
createArchiPlot2.5610.0482.619
createDimRedPlotData0.7300.0170.747
createGeneAgePlot0.2240.0030.230
createLongMatrix0.0170.0070.026
createPercentageDistributionData0.0810.0150.097
createProfileFromOma0.0000.0010.000
createUnrootedTree0.0130.0010.014
createVarDistPlot0.1500.0040.153
createVariableDistributionData0.0080.0030.012
createVariableDistributionDataSubset0.0080.0010.010
dataCustomizedPlot0.0300.0020.032
dataFeatureTaxGroup0.0140.0020.016
dataMainPlot0.0400.0080.047
dataVarDistTaxGroup0.0050.0020.007
dimReduction0.5080.0100.526
estimateGeneAge0.0730.0080.084
fastaParser0.0200.0020.023
featureDistTaxPlot0.1480.0020.152
filterProfileData0.1040.0210.127
fromInputToProfile0.1610.0110.189
geneAgePlotDf0.0090.0000.009
generateSinglePlot0.4090.0050.420
getAllDomainsOma0.0000.0010.000
getAllFastaOma0.0000.0000.001
getCommonAncestor0.0320.0050.036
getCoreGene0.0990.0120.115
getDataClustering0.0180.0030.023
getDataForOneOma000
getDendrogram0.0480.0030.051
getDistanceMatrix0.0180.0010.019
getDomainFolder0.0010.0010.001
getFastaFromFasInput0.0150.0010.017
getFastaFromFile0.0100.0010.011
getFastaFromFolder0.0080.0010.008
getIDsRank0.0180.0020.021
getInputTaxaID0.0030.0010.004
getInputTaxaName0.0110.0030.015
getNameList0.0390.0190.058
getOmaDataForOneOrtholog0.0010.0000.000
getOmaDomainFromURL000
getOmaMembers000
getQualColForVector0.0000.0000.001
getSelectedFastaOma000
getSelectedTaxonNames0.0190.0060.025
getTaxHierarchy0.0150.0020.016
getTaxonomyInfo0.0120.0020.014
getTaxonomyMatrix0.0950.0840.182
getTaxonomyRanks0.0010.0000.000
gridArrangeSharedLegend0.0000.0010.000
groupLabelDimRedData0.0570.0070.065
heatmapPlotting0.2790.0040.285
heatmapPlottingFast4.8580.2134.875
highlightProfilePlot0.3330.0070.341
id2name0.0050.0010.006
joinPlotMergeLegends0.5880.0240.613
linearizeArchitecture0.0080.0010.009
mainTaxonomyRank0.0000.0010.000
modifyFeatureName0.0190.0130.032
pairDomainPlotting0.4160.0060.422
parseDomainInput0.0180.0120.031
parseInfoProfile0.1150.0140.129
plotDimRed1.0240.0211.048
plotDimRed3D1.0190.0361.055
prepareDimRedData0.0550.0060.061
processNcbiTaxonomy0.0000.0000.001
processOrthoID0.1410.0680.267
qualitativeColours000
rankIndexing0.0660.0040.070
reduceProfile0.0430.0010.044
resolveOverlapFeatures0.0170.0010.017
runPhyloProfile0.0000.0000.001
singleDomainPlotting0.1840.0030.188
sortDomains0.0080.0010.009
sortDomainsByList0.0090.0010.010
sortInputTaxa0.0310.0070.037
sortTaxaFromTree0.0110.0010.012
taxonomyTableCreator0.0840.0040.088
varDistTaxPlot0.8060.0120.819
wideToLong0.0130.0060.019
xmlParser0.0170.0030.019