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This page was generated on 2025-08-04 11:46 -0400 (Mon, 04 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4823
palomino7Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4565
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4603
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4544
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: 2025-07-31 13:40 -0400 (Thu, 31 Jul 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 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    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: 2025-08-02 05:57:23 -0400 (Sat, 02 Aug 2025)
EndedAt: 2025-08-02 06:00:28 -0400 (Sat, 02 Aug 2025)
EllapsedTime: 184.5 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 4.794  0.217   4.816
* 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 
  7.301   0.550   7.874 

Example timings

PhyloProfile.Rcheck/PhyloProfile-Ex.timings

nameusersystemelapsed
addDimRedTaxaColors0.8220.0550.880
addFeatureColors0.0350.0040.039
addRankDivisionPlot0.7530.0340.787
calcPresSpec0.0380.0020.041
checkColorPalette0.0010.0000.000
checkInputValidity0.0050.0010.006
checkNewick0.0030.0000.003
checkOmaID000
checkOverlapDomains0.0160.0010.017
clusterDataDend0.0190.0020.020
compareMedianTaxonGroups0.0250.0030.029
compareTaxonGroups0.0330.0040.036
createArchiPlot2.6490.0482.702
createDimRedPlotData0.7350.0200.756
createGeneAgePlot0.2150.0030.218
createLongMatrix0.0170.0060.023
createPercentageDistributionData0.0770.0140.092
createProfileFromOma0.0000.0000.001
createUnrootedTree0.0130.0010.014
createVarDistPlot0.1490.0030.152
createVariableDistributionData0.0090.0040.012
createVariableDistributionDataSubset0.0080.0020.010
dataCustomizedPlot0.0340.0020.036
dataFeatureTaxGroup0.0150.0020.017
dataMainPlot0.0400.0080.048
dataVarDistTaxGroup0.0060.0020.008
dimReduction0.7320.0180.749
estimateGeneAge0.1320.0140.146
fastaParser0.0330.0010.035
featureDistTaxPlot0.1880.0030.191
filterProfileData0.1220.0280.150
fromInputToProfile0.1770.0110.188
geneAgePlotDf0.0090.0000.009
generateSinglePlot0.3840.0060.390
getAllDomainsOma0.0000.0000.001
getAllFastaOma0.0000.0000.001
getCommonAncestor0.0320.0040.037
getCoreGene0.0980.0130.111
getDataClustering0.0160.0020.019
getDataForOneOma000
getDendrogram0.0460.0030.049
getDistanceMatrix0.0160.0010.017
getDomainFolder0.0010.0000.001
getFastaFromFasInput0.0140.0010.015
getFastaFromFile0.0100.0010.011
getFastaFromFolder0.0070.0020.009
getIDsRank0.0190.0020.022
getInputTaxaID0.0030.0020.004
getInputTaxaName0.0130.0040.016
getNameList0.0400.0210.062
getOmaDataForOneOrtholog000
getOmaDomainFromURL000
getOmaMembers000
getQualColForVector0.0000.0000.001
getSelectedFastaOma000
getSelectedTaxonNames0.0210.0050.026
getTaxHierarchy0.0150.0010.016
getTaxonomyInfo0.0130.0010.014
getTaxonomyMatrix0.0950.0730.168
getTaxonomyRanks0.0010.0010.000
gridArrangeSharedLegend000
groupLabelDimRedData0.0530.0060.060
heatmapPlotting0.2620.0040.266
heatmapPlottingFast4.7940.2174.816
highlightProfilePlot0.2920.0090.303
id2name0.0060.0010.006
joinPlotMergeLegends0.5670.0320.606
linearizeArchitecture0.0080.0000.009
mainTaxonomyRank0.0000.0000.001
modifyFeatureName0.0200.0140.034
pairDomainPlotting0.3290.0050.337
parseDomainInput0.0070.0040.012
parseInfoProfile0.0700.0090.078
plotDimRed0.5390.0130.558
plotDimRed3D1.0060.0381.056
prepareDimRedData0.0580.0060.064
processNcbiTaxonomy0.0000.0000.001
processOrthoID0.1100.0580.213
qualitativeColours0.0010.0000.000
rankIndexing0.0410.0020.045
reduceProfile0.0430.0010.044
resolveOverlapFeatures0.0170.0010.019
runPhyloProfile0.0010.0000.000
singleDomainPlotting0.1400.0020.144
sortDomains0.0040.0000.005
sortDomainsByList0.0070.0000.008
sortInputTaxa0.0260.0060.033
sortTaxaFromTree0.0060.0010.006
taxonomyTableCreator0.0450.0020.048
varDistTaxPlot0.7600.0070.769
wideToLong0.0130.0070.020
xmlParser0.0180.0030.022