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This page was generated on 2025-08-04 11:41 -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 nebbiolo1

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: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:PhyloProfile.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings PhyloProfile_2.0.6.tar.gz
StartedAt: 2025-08-04 01:23:57 -0400 (Mon, 04 Aug 2025)
EndedAt: 2025-08-04 01:26:46 -0400 (Mon, 04 Aug 2025)
EllapsedTime: 169.2 seconds
RetCode: 0
Status:   OK  
CheckDir: PhyloProfile.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:PhyloProfile.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings PhyloProfile_2.0.6.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/PhyloProfile.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 24.04.2 LTS
* using session charset: UTF-8
* 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 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
* 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-3.21-bioc/R/bin/R CMD INSTALL PhyloProfile
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-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 (2025-06-13) -- "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 
  6.034   0.393   6.416 

Example timings

PhyloProfile.Rcheck/PhyloProfile-Ex.timings

nameusersystemelapsed
addDimRedTaxaColors0.6270.0330.662
addFeatureColors0.0290.0060.034
addRankDivisionPlot0.6820.0400.722
calcPresSpec0.0300.0030.032
checkColorPalette0.0010.0000.001
checkInputValidity0.0030.0010.004
checkNewick0.0010.0010.002
checkOmaID0.0010.0000.001
checkOverlapDomains0.0120.0000.013
clusterDataDend0.0150.0010.016
compareMedianTaxonGroups0.0210.0010.022
compareTaxonGroups0.0260.0030.029
createArchiPlot2.2930.0912.384
createDimRedPlotData0.5520.0150.567
createGeneAgePlot0.1880.0010.189
createLongMatrix0.0090.0100.019
createPercentageDistributionData0.0640.0020.066
createProfileFromOma000
createUnrootedTree0.0100.0000.011
createVarDistPlot0.1390.0000.140
createVariableDistributionData0.0070.0020.008
createVariableDistributionDataSubset0.0060.0010.007
dataCustomizedPlot0.0290.0040.032
dataFeatureTaxGroup0.0120.0010.013
dataMainPlot0.0370.0070.043
dataVarDistTaxGroup0.0040.0020.006
dimReduction0.5690.0130.582
estimateGeneAge0.1020.0070.108
fastaParser0.0270.0020.029
featureDistTaxPlot0.1750.0020.177
filterProfileData0.0930.0290.121
fromInputToProfile0.1500.0020.151
geneAgePlotDf0.0070.0000.008
generateSinglePlot0.3450.0000.345
getAllDomainsOma0.0000.0000.001
getAllFastaOma0.0010.0000.000
getCommonAncestor0.0260.0050.030
getCoreGene0.0810.0060.087
getDataClustering0.0150.0000.015
getDataForOneOma000
getDendrogram0.0400.0010.042
getDistanceMatrix0.0140.0000.015
getDomainFolder0.0000.0010.000
getFastaFromFasInput0.0120.0010.012
getFastaFromFile0.0090.0000.009
getFastaFromFolder0.0060.0010.007
getIDsRank0.0160.0020.019
getInputTaxaID0.0010.0010.003
getInputTaxaName0.010.000.01
getNameList0.0270.0230.049
getOmaDataForOneOrtholog0.0010.0000.000
getOmaDomainFromURL000
getOmaMembers0.0000.0010.000
getQualColForVector000
getSelectedFastaOma0.0000.0000.001
getSelectedTaxonNames0.0130.0010.016
getTaxHierarchy0.0120.0010.014
getTaxonomyInfo0.0120.0010.012
getTaxonomyMatrix0.0710.0910.161
getTaxonomyRanks0.0000.0000.001
gridArrangeSharedLegend0.0000.0000.001
groupLabelDimRedData0.0470.0020.049
heatmapPlotting0.2460.0010.246
heatmapPlottingFast3.6750.4083.793
highlightProfilePlot0.2830.0060.289
id2name0.0030.0020.004
joinPlotMergeLegends0.5260.0060.535
linearizeArchitecture0.0070.0000.008
mainTaxonomyRank0.0000.0010.001
modifyFeatureName0.0110.0170.029
pairDomainPlotting0.3900.0010.391
parseDomainInput0.0140.0120.027
parseInfoProfile0.0930.0030.095
plotDimRed0.8380.0120.850
plotDimRed3D0.8080.0240.832
prepareDimRedData0.0470.0020.049
processNcbiTaxonomy0.0010.0000.001
processOrthoID0.1170.0300.168
qualitativeColours000
rankIndexing0.0540.0020.056
reduceProfile0.0410.0010.042
resolveOverlapFeatures0.0130.0010.015
runPhyloProfile000
singleDomainPlotting0.1740.0010.175
sortDomains0.0060.0020.007
sortDomainsByList0.0070.0020.008
sortInputTaxa0.0250.0020.027
sortTaxaFromTree0.0100.0000.011
taxonomyTableCreator0.0810.0020.084
varDistTaxPlot0.7430.0030.746
wideToLong0.0100.0060.015
xmlParser0.0120.0040.016