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This page was generated on 2024-11-20 12:06 -0500 (Wed, 20 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4481
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4479
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4359
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4539
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
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 1547/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PhyloProfile 1.20.3  (landing page)
Vinh Tran
Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024)
git_url: https://git.bioconductor.org/packages/PhyloProfile
git_branch: RELEASE_3_20
git_last_commit: c0af867
git_last_commit_date: 2024-11-07 08:33:25 -0500 (Thu, 07 Nov 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / 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: 1.20.3
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_1.20.3.tar.gz
StartedAt: 2024-11-20 01:09:34 -0500 (Wed, 20 Nov 2024)
EndedAt: 2024-11-20 01:16:14 -0500 (Wed, 20 Nov 2024)
EllapsedTime: 400.6 seconds
RetCode: 0
Status:   OK  
CheckDir: PhyloProfile.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.20.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/PhyloProfile.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* 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 ‘1.20.3’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 OK
* 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
* 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/4.4-x86_64/Resources/library’
* installing *source* package ‘PhyloProfile’ ...
** 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 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 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 20 ]
> 
> proc.time()
   user  system elapsed 
  6.259   0.474   6.771 

Example timings

PhyloProfile.Rcheck/PhyloProfile-Ex.timings

nameusersystemelapsed
addFeatureColors0.0430.0050.049
addRankDivisionPlot1.0260.0421.070
addUmapTaxaColors0.9360.0380.983
calcPresSpec0.0370.0020.038
checkColorPalette0.0010.0000.000
checkInputValidity0.0030.0010.004
checkNewick0.0020.0010.003
checkOmaID000
checkOverlapDomains0.0120.0010.013
clusterDataDend0.0100.0000.011
compareMedianTaxonGroups0.0170.0020.019
compareTaxonGroups0.0240.0020.026
createArchiPlot1.6620.0221.692
createGeneAgePlot0.1750.0050.183
createLongMatrix0.0130.0060.019
createPercentageDistributionData0.0780.0100.088
createProfileFromOma000
createUmapPlotData1.3740.0221.402
createUnrootedTree0.0080.0000.009
createVarDistPlot0.1160.0020.120
createVariableDistributionData0.0050.0030.008
createVariableDistributionDataSubset0.0050.0010.007
dataCustomizedPlot0.0120.0010.013
dataFeatureTaxGroup0.0100.0020.011
dataMainPlot0.0170.0070.025
dataVarDistTaxGroup0.0050.0020.006
estimateGeneAge0.0910.0090.100
fastaParser0.0280.0020.031
featureDistTaxPlot0.1550.0040.159
filterProfileData0.0800.0220.104
fromInputToProfile0.0750.0110.087
geneAgePlotDf0.0070.0000.006
generateSinglePlot0.2960.0050.304
getAllDomainsOma0.0000.0000.001
getAllFastaOma000
getCommonAncestor0.0210.0030.024
getCoreGene0.0650.0080.073
getDataClustering0.0090.0020.010
getDataForOneOma000
getDendrogram0.0310.0030.033
getDistanceMatrix0.0090.0010.010
getDomainFolder0.0000.0000.001
getFastaFromFasInput0.0120.0000.012
getFastaFromFile0.0080.0010.010
getFastaFromFolder0.0060.0010.008
getIDsRank0.0150.0020.017
getInputTaxaID0.0020.0010.003
getInputTaxaName0.0080.0030.011
getNameList0.0160.0170.034
getOmaDataForOneOrtholog000
getOmaDomainFromURL0.0000.0000.001
getOmaMembers000
getQualColForVector000
getSelectedFastaOma000
getSelectedTaxonNames0.0120.0030.016
getTaxHierarchy0.0120.0010.013
getTaxonomyInfo0.0120.0010.014
getTaxonomyMatrix0.0790.0640.147
getTaxonomyRanks0.0000.0000.001
gridArrangeSharedLegend000
groupLabelUmapData0.0380.0040.044
heatmapPlotting0.1840.0020.187
heatmapPlottingFast3.0050.1382.901
highlightProfilePlot0.2220.0070.230
id2name0.0030.0000.003
joinPlotMergeLegends0.4210.0330.456
linearizeArchitecture0.0070.0000.007
mainTaxonomyRank0.0000.0000.001
modifyFeatureName0.0140.0140.028
pairDomainPlotting0.3180.0020.320
parseDomainInput0.0130.0100.024
parseInfoProfile0.0610.0160.078
plotUmap1.0980.0261.127
plotUmap3D1.0620.0471.112
prepareUmapData0.0370.0050.042
processNcbiTaxonomy000
processOrthoID0.0930.0560.202
qualitativeColours0.0000.0000.001
rankIndexing0.0330.0010.035
reduceProfile0.0100.0050.016
resolveOverlapFeatures0.0120.0010.013
runPhyloProfile000
singleDomainPlotting0.1550.0020.158
sortDomains0.0060.0010.006
sortDomainsByList0.0080.0020.009
sortInputTaxa0.0200.0050.026
sortTaxaFromTree0.0080.0010.009
taxonomyTableCreator0.0650.0040.069
umapClustering0.8880.0150.907
umapClustering3D0.8520.0070.859
varDistTaxPlot0.6070.0060.616
wideToLong0.0090.0050.014
xmlParser0.0150.0030.018