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This page was generated on 2022-05-16 11:08:11 -0400 (Mon, 16 May 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4379
palomino3Windows Server 2022 Datacenterx644.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" 4153
merida1macOS 10.14.6 Mojavex86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4220
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

CHECK results for PhyloProfile on merida1


To the developers/maintainers of the PhyloProfile package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1452/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PhyloProfile 1.10.1  (landing page)
Vinh Tran
Snapshot Date: 2022-05-15 13:55:12 -0400 (Sun, 15 May 2022)
git_url: https://git.bioconductor.org/packages/PhyloProfile
git_branch: RELEASE_3_15
git_last_commit: bbf42d9
git_last_commit_date: 2022-04-29 05:56:42 -0400 (Fri, 29 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: PhyloProfile
Version: 1.10.1
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_1.10.1.tar.gz
StartedAt: 2022-05-16 06:00:52 -0400 (Mon, 16 May 2022)
EndedAt: 2022-05-16 06:05:17 -0400 (Mon, 16 May 2022)
EllapsedTime: 265.7 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_1.10.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/PhyloProfile.Rcheck’
* using R version 4.2.0 (2022-04-22)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PhyloProfile/DESCRIPTION’ ... OK
* this is package ‘PhyloProfile’ version ‘1.10.1’
* 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 R 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 in ‘inst/doc’ ... 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/4.2/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 4.2.0 (2022-04-22) -- "Vigorous Calisthenics"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

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 
 12.456   0.707  13.156 

Example timings

PhyloProfile.Rcheck/PhyloProfile-Ex.timings

nameusersystemelapsed
calcPresSpec0.0540.0040.058
checkInputValidity0.0160.0010.017
checkNewick0.0040.0000.005
checkOmaID0.0000.0000.001
clusterDataDend0.0500.0030.053
compareMedianTaxonGroups0.0510.0030.053
compareTaxonGroups0.0720.0040.076
createArchiPlot1.4460.0101.459
createGeneAgePlot0.2900.0020.292
createLongMatrix0.0380.0070.046
createPercentageDistributionData0.1790.0310.210
createProfileFromOma000
createRootedTree0.0260.0010.028
createVarDistPlot0.2890.0030.293
createVariableDistributionData0.0130.0040.017
createVariableDistributionDataSubset0.0150.0020.018
dataCustomizedPlot0.0200.0020.022
dataFeatureTaxGroup0.0260.0020.027
dataMainPlot0.0230.0050.030
dataVarDistTaxGroup0.0090.0020.010
estimateGeneAge0.2560.0390.296
fastaParser0.0750.0020.077
featureDistTaxPlot0.3430.0070.354
filterProfileData0.2190.0560.277
fromInputToProfile0.2030.0270.231
geneAgePlotDf0.0060.0000.007
generateSinglePlot0.5920.0210.613
getAllDomainsOma000
getAllFastaOma000
getCommonAncestor0.0800.0140.094
getCoreGene0.1640.0300.194
getDataClustering0.0180.0020.019
getDataForOneOma0.0000.0000.001
getDendrogram0.0790.0020.086
getDistanceMatrix0.0240.0010.025
getDomainFolder0.0010.0000.000
getFastaFromFasInput0.0290.0000.029
getFastaFromFile0.0180.0010.019
getFastaFromFolder0.0130.0010.015
getIDsRank0.0500.0030.053
getInputTaxaID0.0030.0010.004
getInputTaxaName0.0190.0040.023
getNameList0.0360.0180.053
getOmaDataForOneOrtholog000
getOmaDomainFromURL0.0000.0000.001
getOmaMembers000
getQualColForVector000
getSelectedFastaOma0.0010.0000.000
getSelectedTaxonNames0.0290.0040.035
getTaxonomyInfo0.0250.0010.026
getTaxonomyMatrix0.1810.0750.256
getTaxonomyRanks000
gridArrangeSharedLegend0.9580.0120.974
heatmapPlotting0.3770.0030.380
highlightProfilePlot0.4370.0160.453
mainTaxonomyRank0.0000.0000.001
pairDomainPlotting0.0000.0000.001
parseDomainInput0.0280.0110.038
parseInfoProfile0.6890.0410.732
processNcbiTaxonomy0.1400.0650.237
qualitativeColours000
rankIndexing000
reduceProfile0.0210.0060.027
runPhyloProfile0.1220.0330.157
singleDomainPlotting000
sortDomains000
sortInputTaxa0.1130.0210.135
sortTaxaFromTree0.0270.0010.027
taxonomyTableCreator0.2180.0070.227
varDistTaxPlot1.2170.0381.257
wideToLong0.0250.0060.031
xmlParser0.0350.0020.038