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This page was generated on 2024-11-20 12:08 -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 kunpeng2

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: PhyloProfile
Version: 1.20.3
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:PhyloProfile.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings PhyloProfile_1.20.3.tar.gz
StartedAt: 2024-11-20 11:00:26 -0000 (Wed, 20 Nov 2024)
EndedAt: 2024-11-20 11:04:32 -0000 (Wed, 20 Nov 2024)
EllapsedTime: 245.4 seconds
RetCode: 0
Status:   OK  
CheckDir: PhyloProfile.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:PhyloProfile.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings PhyloProfile_1.20.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/PhyloProfile.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* 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 ... 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 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 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:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL PhyloProfile
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.4.1/site-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: aarch64-unknown-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 20 ]
> 
> proc.time()
   user  system elapsed 
 10.016   0.423  10.362 

Example timings

PhyloProfile.Rcheck/PhyloProfile-Ex.timings

nameusersystemelapsed
addFeatureColors0.0600.0040.066
addRankDivisionPlot1.6350.0921.731
addUmapTaxaColors1.6270.0441.676
calcPresSpec0.0550.0040.059
checkColorPalette0.0010.0000.001
checkInputValidity0.0050.0000.006
checkNewick0.0030.0000.002
checkOmaID000
checkOverlapDomains0.0150.0040.019
clusterDataDend0.0140.0030.018
compareMedianTaxonGroups0.0320.0000.033
compareTaxonGroups0.0390.0040.043
createArchiPlot3.1500.0323.189
createGeneAgePlot0.2730.0080.282
createLongMatrix0.0120.0040.016
createPercentageDistributionData0.1180.0040.124
createProfileFromOma000
createUmapPlotData2.2720.0682.345
createUnrootedTree0.0170.0000.017
createVarDistPlot0.2030.0000.203
createVariableDistributionData0.0060.0000.007
createVariableDistributionDataSubset0.0090.0000.008
dataCustomizedPlot0.0220.0000.021
dataFeatureTaxGroup0.0090.0070.016
dataMainPlot0.0260.0000.026
dataVarDistTaxGroup0.0060.0000.006
estimateGeneAge0.1510.0040.155
fastaParser0.0450.0000.046
featureDistTaxPlot0.2850.0080.294
filterProfileData0.1120.0120.125
fromInputToProfile0.1250.0040.129
geneAgePlotDf0.010.000.01
generateSinglePlot0.5250.0120.586
getAllDomainsOma000
getAllFastaOma000
getCommonAncestor0.0450.0000.045
getCoreGene0.1080.0000.109
getDataClustering0.0150.0000.016
getDataForOneOma000
getDendrogram0.0550.0000.055
getDistanceMatrix0.0160.0000.016
getDomainFolder0.0010.0000.001
getFastaFromFasInput0.0190.0000.019
getFastaFromFile0.0090.0030.014
getFastaFromFolder0.0090.0000.010
getIDsRank0.0260.0000.026
getInputTaxaID0.0020.0000.002
getInputTaxaName0.0120.0000.013
getNameList0.0090.0080.018
getOmaDataForOneOrtholog000
getOmaDomainFromURL000
getOmaMembers000
getQualColForVector000
getSelectedFastaOma000
getSelectedTaxonNames0.0190.0000.018
getTaxHierarchy0.0190.0000.019
getTaxonomyInfo0.0180.0000.018
getTaxonomyMatrix0.1080.0080.116
getTaxonomyRanks0.0010.0000.000
gridArrangeSharedLegend000
groupLabelUmapData0.0630.0000.063
heatmapPlotting0.3450.0040.350
heatmapPlottingFast4.5600.1564.581
highlightProfilePlot0.3930.0070.402
id2name0.0050.0010.005
joinPlotMergeLegends0.7590.0120.773
linearizeArchitecture0.0130.0000.013
mainTaxonomyRank000
modifyFeatureName0.0150.0000.014
pairDomainPlotting0.5800.0000.582
parseDomainInput0.0140.0000.014
parseInfoProfile0.0840.0070.091
plotUmap2.0150.0192.038
plotUmap3D1.9520.0041.960
prepareUmapData0.0600.0010.061
processNcbiTaxonomy000
processOrthoID0.1350.0100.173
qualitativeColours000
rankIndexing0.0630.0000.064
reduceProfile0.0140.0000.015
resolveOverlapFeatures0.0190.0000.020
runPhyloProfile000
singleDomainPlotting0.3120.0000.314
sortDomains0.0090.0000.009
sortDomainsByList0.0110.0000.011
sortInputTaxa0.0360.0000.036
sortTaxaFromTree0.0160.0000.017
taxonomyTableCreator0.1190.0000.121
umapClustering1.6210.0081.632
umapClustering3D1.6070.0201.631
varDistTaxPlot1.2120.0041.219
wideToLong0.010.000.01
xmlParser0.0160.0040.021