Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:08:31 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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 machv2


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 1414/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PhyloProfile 1.8.6  (landing page)
Vinh Tran
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/PhyloProfile
git_branch: RELEASE_3_14
git_last_commit: fe576e8
git_last_commit_date: 2022-02-17 04:11:27 -0400 (Thu, 17 Feb 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: PhyloProfile
Version: 1.8.6
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_1.8.6.tar.gz
StartedAt: 2022-04-12 16:44:31 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 16:48:19 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 228.4 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_1.8.6.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/PhyloProfile.Rcheck’
* using R version 4.1.3 (2022-03-10)
* 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 ‘1.8.6’
* 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/4.1/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 4.1.3 (2022-03-10) -- "One Push-Up"
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 
 10.783   0.632  11.396 

Example timings

PhyloProfile.Rcheck/PhyloProfile-Ex.timings

nameusersystemelapsed
calcPresSpec0.0310.0030.034
checkInputValidity0.0140.0010.016
checkNewick0.0030.0010.004
checkOmaID000
clusterDataDend0.0470.0030.050
compareMedianTaxonGroups0.0480.0040.051
compareTaxonGroups0.0540.0030.056
createArchiPlot1.1630.0081.173
createGeneAgePlot0.2550.0050.260
createLongMatrix0.0390.0150.054
createPercentageDistributionData0.1480.0350.183
createProfileFromOma0.0010.0000.000
createRootedTree0.0270.0020.028
createVarDistPlot0.2370.0030.240
createVariableDistributionData0.0120.0080.020
createVariableDistributionDataSubset0.0150.0030.017
dataCustomizedPlot0.0150.0020.018
dataFeatureTaxGroup0.0230.0020.025
dataMainPlot0.0230.0120.035
dataVarDistTaxGroup0.0080.0020.010
estimateGeneAge0.2160.0300.246
fastaParser0.0480.0010.050
featureDistTaxPlot0.2900.0030.294
filterProfileData0.1860.0640.250
fromInputToProfile0.1890.0370.226
geneAgePlotDf0.0070.0010.008
generateSinglePlot0.5150.0200.534
getAllDomainsOma0.0000.0010.000
getAllFastaOma0.0010.0000.001
getCommonAncestor0.0660.0120.077
getCoreGene0.1580.0350.192
getDataClustering0.0140.0020.016
getDataForOneOma000
getDendrogram0.0640.0020.068
getDistanceMatrix0.0160.0020.018
getDomainFolder000
getFastaFromFasInput0.0240.0000.026
getFastaFromFile0.0150.0010.016
getFastaFromFolder0.0120.0010.013
getIDsRank0.0450.0040.049
getInputTaxaID0.0020.0010.003
getInputTaxaName0.0150.0030.017
getNameList0.0300.0380.068
getOmaDataForOneOrtholog000
getOmaDomainFromURL0.0000.0000.001
getOmaMembers000
getQualColForVector0.0000.0000.001
getSelectedFastaOma0.0000.0000.001
getSelectedTaxonNames0.0250.0050.031
getTaxonomyInfo0.0240.0030.026
getTaxonomyMatrix0.1720.1430.316
getTaxonomyRanks0.0000.0000.001
gridArrangeSharedLegend0.9280.0160.946
heatmapPlotting0.3110.0040.314
highlightProfilePlot0.3150.0130.382
mainTaxonomyRank0.0010.0020.002
pairDomainPlotting0.0000.0010.001
parseDomainInput0.0270.0260.086
parseInfoProfile0.1630.0420.205
processNcbiTaxonomy0.1190.0530.213
qualitativeColours000
rankIndexing0.0000.0010.000
reduceProfile0.0190.0080.026
runPhyloProfile0.1110.0340.148
singleDomainPlotting0.0000.0010.001
sortDomains0.0000.0000.001
sortInputTaxa0.1310.0210.152
sortTaxaFromTree0.0270.0020.029
taxonomyTableCreator0.1970.0090.206
varDistTaxPlot1.4920.0201.514
wideToLong0.0230.0120.036
xmlParser0.0300.0050.036