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CHECK report for PhyloProfile on malbec2

This page was generated on 2020-10-17 11:55:23 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE PhyloProfile PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1308/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PhyloProfile 1.2.8
Vinh Tran
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/PhyloProfile
Branch: RELEASE_3_11
Last Commit: 9e60604
Last Changed Date: 2020-07-21 11:25:05 -0400 (Tue, 21 Jul 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: PhyloProfile
Version: 1.2.8
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:PhyloProfile.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings PhyloProfile_1.2.8.tar.gz
StartedAt: 2020-10-17 04:05:40 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 04:08:21 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 161.1 seconds
RetCode: 0
Status:  OK 
CheckDir: PhyloProfile.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:PhyloProfile.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings PhyloProfile_1.2.8.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/PhyloProfile.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘1.2.8’
* 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-3.11-bioc/R/bin/R CMD INSTALL PhyloProfile
###
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* installing to library ‘/home/biocbuild/bbs-3.11-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 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 20 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  8.283   0.283   8.594 

Example timings

PhyloProfile.Rcheck/PhyloProfile-Ex.timings

nameusersystemelapsed
calcPresSpec0.0480.0000.048
checkInputValidity0.0140.0000.017
checkNewick0.0040.0000.004
checkOmaID000
clusterDataDend0.0460.0000.047
compareMedianTaxonGroups0.0490.0000.049
compareTaxonGroups0.0610.0040.065
createArchiPlot0.7710.0000.771
createGeneAgePlot0.2640.0000.263
createLongMatrix0.0390.0000.039
createPercentageDistributionData0.6030.0160.620
createProfileFromOma0.0000.0010.001
createRootedTree0.0200.0010.021
createVarDistPlot0.2350.0000.236
createVariableDistributionData0.0100.0040.014
createVariableDistributionDataSubset0.0150.0000.016
dataCustomizedPlot0.0470.0000.047
dataFeatureTaxGroup0.0230.0000.023
dataMainPlot0.0540.0120.067
dataVarDistTaxGroup0.0050.0040.008
estimateGeneAge0.0820.0040.087
fastaParser0.0650.0040.069
featureDistTaxPlot0.2610.0160.278
filterProfileData0.0260.0040.030
fromInputToProfile0.1980.0120.211
geneAgePlotDf0.0060.0000.006
generateSinglePlot0.4440.0000.444
getAllDomainsOma000
getAllFastaOma000
getCommonAncestor0.0630.0000.063
getCoreGene0.0180.0000.018
getDataClustering0.0230.0000.023
getDataForOneOma0.0010.0000.001
getDendrogram0.0710.0000.071
getDistanceMatrix0.0210.0000.020
getDomainFolder000
getFastaFromFasInput0.0260.0000.026
getFastaFromFile0.0160.0000.017
getFastaFromFolder0.0140.0000.430
getIDsRank0.0430.0000.051
getInputTaxaID0.0040.0000.004
getInputTaxaName0.0170.0030.020
getNameList0.0400.0080.048
getOmaDataForOneOrtholog000
getOmaDomainFromURL000
getOmaMembers000
getQualColForVector000
getSelectedFastaOma0.0000.0000.001
getSelectedTaxonNames0.0330.0000.033
getTaxonomyInfo0.0130.0000.014
getTaxonomyMatrix0.1830.0360.218
getTaxonomyRanks0.0000.0000.001
gridArrangeSharedLegend0.7240.0360.759
heatmapPlotting0.4750.0000.475
highlightProfilePlot0.5360.0040.540
mainTaxonomyRank0.0000.0000.001
pairDomainPlotting0.0010.0000.001
parseDomainInput0.0310.0000.031
parseInfoProfile0.1710.0160.186
processNcbiTaxonomy0.1090.0470.754
qualitativeColours000
rankIndexing000
reduceProfile0.0190.0060.026
runPhyloProfile0.0880.0560.145
singleDomainPlotting0.0000.0000.001
sortDomains000
sortInputTaxa0.1150.0200.134
sortTaxaFromTree0.0240.0000.024
taxonomyTableCreator0.1810.0120.202
varDistTaxPlot0.9500.0160.965
wideToLong0.0160.0080.025
xmlParser0.0340.0000.033