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This page was generated on 2025-10-17 12:04 -0400 (Fri, 17 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4887
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4677
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4622
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4632
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 1588/2353HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PhyloProfile 2.1.12  (landing page)
Vinh Tran
Snapshot Date: 2025-10-16 13:45 -0400 (Thu, 16 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  UNNEEDED, same version is already published
lconwaymacOS 12.7.6 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 nebbiolo2

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: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:PhyloProfile.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings PhyloProfile_2.1.12.tar.gz
StartedAt: 2025-10-17 04:17:07 -0400 (Fri, 17 Oct 2025)
EndedAt: 2025-10-17 04:20:14 -0400 (Fri, 17 Oct 2025)
EllapsedTime: 187.1 seconds
RetCode: 0
Status:   OK  
CheckDir: PhyloProfile.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:PhyloProfile.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings PhyloProfile_2.1.12.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/PhyloProfile.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* 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 loading without being on the library search path ... 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 4.665  0.424   4.801
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

PhyloProfile.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL PhyloProfile
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-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 (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 
  6.913   0.466   7.372 

Example timings

PhyloProfile.Rcheck/PhyloProfile-Ex.timings

nameusersystemelapsed
addDimRedTaxaColors0.7010.0420.743
addFeatureColors0.0260.0030.030
addRankDivisionPlot1.5890.4572.048
calcPresSpec0.0400.0000.041
checkColorPalette000
checkInputValidity0.0020.0010.004
checkNewick0.0030.0010.002
checkOmaID000
checkOverlapDomains0.0150.0000.015
clusterDataDend0.0160.0000.017
compareMedianTaxonGroups0.0200.0050.027
compareTaxonGroups0.0260.0050.031
createArchiPlot2.1010.1652.266
createDimRedPlotData0.5530.0410.592
createGeneAgePlot0.3060.0040.310
createLongMatrix0.0120.0000.012
createPercentageDistributionData0.0630.0010.065
createProfileFromOma000
createUnrootedTree0.0100.0020.011
createVarDistPlot0.2520.0020.254
createVariableDistributionData0.0040.0020.006
createVariableDistributionDataSubset0.0060.0000.007
dataCustomizedPlot0.0260.0020.029
dataFeatureTaxGroup0.0110.0010.013
dataMainPlot0.0330.0010.034
dataVarDistTaxGroup0.0040.0010.004
dimReduction0.5900.0280.618
estimateGeneAge0.1210.0030.123
fastaParser0.0300.0050.036
featureDistTaxPlot0.3080.0020.310
filterProfileData0.1160.0040.120
fromInputToProfile0.1530.0040.157
geneAgePlotDf0.0080.0000.008
generateSinglePlot0.4570.0240.481
getAllDomainsOma000
getAllFastaOma000
getCommonAncestor0.0300.0020.032
getCoreGene0.0840.0110.095
getDataClustering0.0130.0040.017
getDataForOneOma000
getDendrogram0.0430.0020.045
getDistanceMatrix0.0170.0000.017
getDomainFolder0.0010.0000.001
getFastaFromFasInput0.0150.0000.015
getFastaFromFile0.0090.0010.010
getFastaFromFolder0.0060.0010.007
getIDsRank0.0170.0020.019
getInputTaxaID0.0020.0000.002
getInputTaxaName0.010.000.01
getNameList0.0140.0010.015
getOmaDataForOneOrtholog000
getOmaDomainFromURL000
getOmaMembers000
getQualColForVector0.0010.0000.000
getSelectedFastaOma0.0000.0000.001
getSelectedTaxonNames0.0160.0000.016
getTaxHierarchy0.0140.0000.014
getTaxonomyInfo0.0120.0000.012
getTaxonomyMatrix0.0680.0100.079
getTaxonomyRanks000
gridArrangeSharedLegend000
groupLabelDimRedData0.0640.0030.068
heatmapPlotting0.4090.0050.414
heatmapPlottingFast4.6650.4244.801
highlightProfilePlot0.4810.0050.486
id2name0.0040.0000.004
joinPlotMergeLegends0.7760.0030.779
linearizeArchitecture0.0080.0000.008
mainTaxonomyRank000
modifyFeatureName0.0090.0030.012
pairDomainPlotting0.5540.0390.593
parseDomainInput0.0100.0020.012
parseInfoProfile0.0970.0030.100
plotDimRed1.0690.0041.074
plotDimRed3D0.8140.0040.818
prepareDimRedData0.0470.0000.046
processNcbiTaxonomy000
processOrthoID0.1170.0120.140
qualitativeColours000
rankIndexing0.040.000.04
reduceProfile0.0910.0010.091
resolveOverlapFeatures0.0140.0070.021
runPhyloProfile0.0800.0130.093
singleDomainPlotting0.2430.0040.247
sortDomains0.0070.0000.007
sortDomainsByList0.0060.0020.008
sortInputTaxa0.0260.0030.028
sortTaxaFromTree0.0110.0000.011
taxonomyTableCreator0.0920.0050.097
varDistTaxPlot1.0250.0021.027
wideToLong0.0070.0020.008
xmlParser0.0160.0000.016