Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:05:45 -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 nebbiolo2


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: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:PhyloProfile.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings PhyloProfile_1.8.6.tar.gz
StartedAt: 2022-04-12 08:43:26 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 08:45:37 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 130.6 seconds
RetCode: 0
Status:   OK  
CheckDir: PhyloProfile.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:PhyloProfile.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings PhyloProfile_1.8.6.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/PhyloProfile.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-pc-linux-gnu (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

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL PhyloProfile
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/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-pc-linux-gnu (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 
  6.354   0.271   6.609 

Example timings

PhyloProfile.Rcheck/PhyloProfile-Ex.timings

nameusersystemelapsed
calcPresSpec0.0270.0000.027
checkInputValidity0.0070.0000.007
checkNewick0.0020.0000.002
checkOmaID000
clusterDataDend0.0210.0040.025
compareMedianTaxonGroups0.0210.0040.024
compareTaxonGroups0.0340.0000.034
createArchiPlot1.0500.0481.098
createGeneAgePlot0.1460.0080.154
createLongMatrix0.0130.0080.021
createPercentageDistributionData0.0980.0040.102
createProfileFromOma000
createRootedTree0.0110.0000.011
createVarDistPlot0.1420.0000.142
createVariableDistributionData0.0070.0000.007
createVariableDistributionDataSubset0.0090.0000.009
dataCustomizedPlot0.0110.0000.011
dataFeatureTaxGroup0.0120.0000.012
dataMainPlot0.0080.0040.012
dataVarDistTaxGroup0.0050.0000.005
estimateGeneAge0.1130.0080.121
fastaParser0.0360.0000.035
featureDistTaxPlot0.1530.0000.153
filterProfileData0.1020.0040.105
fromInputToProfile0.0900.0040.094
geneAgePlotDf0.0040.0000.003
generateSinglePlot0.2730.0000.273
getAllDomainsOma0.0000.0000.001
getAllFastaOma0.0010.0000.000
getCommonAncestor0.0260.0080.034
getCoreGene0.0660.0200.085
getDataClustering0.0080.0000.008
getDataForOneOma0.0000.0010.000
getDendrogram0.0370.0030.039
getDistanceMatrix0.0130.0000.012
getDomainFolder000
getFastaFromFasInput0.0140.0000.014
getFastaFromFile0.0100.0000.009
getFastaFromFolder0.0080.0000.007
getIDsRank0.0240.0000.024
getInputTaxaID0.0030.0000.003
getInputTaxaName0.0100.0000.009
getNameList0.0180.0000.018
getOmaDataForOneOrtholog0.0000.0000.001
getOmaDomainFromURL000
getOmaMembers0.0000.0000.001
getQualColForVector000
getSelectedFastaOma000
getSelectedTaxonNames0.0180.0040.021
getTaxonomyInfo0.0140.0000.014
getTaxonomyMatrix0.0670.0280.096
getTaxonomyRanks0.0010.0000.000
gridArrangeSharedLegend0.4450.0280.473
heatmapPlotting0.1830.0000.183
highlightProfilePlot0.2090.0040.212
mainTaxonomyRank0.0010.0000.000
pairDomainPlotting000
parseDomainInput0.0080.0040.013
parseInfoProfile0.1060.0040.110
processNcbiTaxonomy0.0620.0180.084
qualitativeColours000
rankIndexing000
reduceProfile0.010.000.01
runPhyloProfile0.0570.0100.067
singleDomainPlotting000
sortDomains0.0000.0010.000
sortInputTaxa0.6300.0070.638
sortTaxaFromTree0.0110.0000.011
taxonomyTableCreator0.1010.0000.101
varDistTaxPlot0.5370.0520.590
wideToLong0.0120.0000.012
xmlParser0.0150.0040.019