Package: PhyloProfile

Version: 1.0.7

Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:PhyloProfile.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings PhyloProfile_1.0.7.tar.gz

StartedAt: 2020-04-15 06:45:55 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 06:48:41 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 165.1 seconds

RetCode: 0

Status:  OK

CheckDir: PhyloProfile.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:PhyloProfile.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings PhyloProfile_1.0.7.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/PhyloProfile.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.0.7’
* 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

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL PhyloProfile
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* installing to library ‘/home/biocbuild/bbs-3.10-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)

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
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 
 13.072   0.280  10.314 

name	user	system	elapsed
calcPresSpec	0.344	0.004	0.346
checkInputValidity	0.012	0.000	0.033
checkNewick	0.004	0.000	0.003
checkOmaID	0	0	0
clusterDataDend	1.140	0.012	0.379
compareMedianTaxonGroups	0.032	0.000	0.035
compareTaxonGroups	0.052	0.000	0.053
createArchiPlot	0.668	0.000	0.853
createGeneAgePlot	0.208	0.000	0.212
createLongMatrix	0.020	0.000	0.022
createPercentageDistributionData	0.136	0.000	0.137
createProfileFromOma	0.000	0.000	0.001
createRootedTree	0.02	0.00	0.02
createVarDistPlot	0.256	0.000	0.258
createVariableDistributionData	0.008	0.004	0.013
createVariableDistributionDataSubset	0.012	0.000	0.013
dataCustomizedPlot	0.268	0.004	0.148
dataFeatureTaxGroup	0.02	0.00	0.02
dataMainPlot	0.260	0.016	0.118
dataVarDistTaxGroup	0.004	0.000	0.008
estimateGeneAge	0.040	0.004	0.047
fastaParser	0.048	0.000	0.044
featureDistTaxPlot	0.244	0.004	0.251
filterProfileData	0.020	0.004	0.029
fromInputToProfile	0.140	0.004	0.159
geneAgePlotDf	0.008	0.000	0.004
generateSinglePlot	0.580	0.000	0.641
getAllDomainsOma	0.000	0.000	0.001
getAllFastaOma	0	0	0
getCommonAncestor	0.036	0.004	0.040
getCoreGene	0.020	0.000	0.019
getDataClustering	0.312	0.004	0.100
getDataForOneOma	0	0	0
getDendrogram	1.188	0.004	0.429
getDistanceMatrix	1.212	0.004	0.499
getDomainFolder	0	0	0
getFastaFromFasInput	0.020	0.000	0.018
getFastaFromFile	0.008	0.000	0.022
getFastaFromFolder	0.004	0.000	0.008
getIDsRank	0.420	0.004	0.157
getInputTaxaID	0.004	0.000	0.004
getInputTaxaName	0.012	0.004	0.017
getNameList	0.024	0.016	0.040
getOmaDataForOneOrtholog	0	0	0
getOmaDomainFromURL	0	0	0
getOmaMembers	0	0	0
getQualColForVector	0	0	0
getSelectedFastaOma	0.004	0.000	0.000
getSelectedTaxonNames	0.020	0.004	0.026
getTaxonomyInfo	0.012	0.000	0.011
getTaxonomyMatrix	0.160	0.032	0.192
getTaxonomyRanks	0.004	0.000	0.001
gridArrangeSharedLegend	0.764	0.000	0.769
heatmapPlotting	1.116	0.004	0.976
highlightProfilePlot	0.836	0.036	0.740
mainTaxonomyRank	0	0	0
pairDomainPlotting	0	0	0
parseDomainInput	0.020	0.008	0.029
parseInfoProfile	0.196	0.012	0.209
processNcbiTaxonomy	0.088	0.048	0.559
qualitativeColours	0	0	0
rankIndexing	0	0	0
reduceProfile	0.024	0.000	0.034
runPhyloprofile	0.080	0.016	0.103
singleDomainPlotting	0.000	0.000	0.001
sortDomains	0	0	0
sortInputTaxa	0.084	0.016	0.101
sortTaxaFromTree	0.012	0.004	0.017
taxonomyTableCreator	3.304	0.016	1.232
varDistTaxPlot	1.032	0.044	1.090
wideToLong	0.024	0.000	0.025
xmlParser	1.204	0.004	0.473