Package: PhyloProfile

Version: 1.1.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:PhyloProfile.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings PhyloProfile_1.1.3.tar.gz

StartedAt: 2020-01-16 07:26:41 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 07:30:31 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 229.0 seconds

RetCode: 0

Status:  OK

CheckDir: PhyloProfile.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:PhyloProfile.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings PhyloProfile_1.1.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/PhyloProfile.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PhyloProfile/DESCRIPTION’ ... OK
* this is package ‘PhyloProfile’ version ‘1.1.3’
* 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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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL PhyloProfile
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/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)

R Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 20 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 12.451   1.941  11.446 

name	user	system	elapsed
calcPresSpec	0.056	0.004	0.059
checkInputValidity	0.019	0.002	0.022
checkNewick	0.004	0.001	0.005
checkOmaID	0.000	0.000	0.001
clusterDataDend	0.156	0.125	0.060
compareMedianTaxonGroups	0.126	0.109	0.040
compareTaxonGroups	0.178	0.156	0.059
createArchiPlot	1.171	0.108	1.107
createGeneAgePlot	0.284	0.003	0.288
createLongMatrix	0.063	0.014	0.076
createPercentageDistributionData	0.163	0.037	0.200
createProfileFromOma	0.000	0.000	0.001
createRootedTree	0.022	0.002	0.023
createVarDistPlot	0.311	0.004	0.347
createVariableDistributionData	0.020	0.006	0.026
createVariableDistributionDataSubset	0.019	0.004	0.023
dataCustomizedPlot	0.189	0.150	0.090
dataFeatureTaxGroup	0.156	0.111	0.058
dataMainPlot	0.340	0.287	0.141
dataVarDistTaxGroup	0.036	0.026	0.015
estimateGeneAge	0.161	0.098	0.080
fastaParser	0.071	0.002	0.073
featureDistTaxPlot	0.354	0.005	0.362
filterProfileData	0.045	0.014	0.058
fromInputToProfile	0.206	0.033	0.240
geneAgePlotDf	0.007	0.000	0.007
generateSinglePlot	0.649	0.009	0.658
getAllDomainsOma	0.001	0.000	0.001
getAllFastaOma	0.001	0.001	0.000
getCommonAncestor	0.041	0.006	0.047
getCoreGene	0.022	0.006	0.028
getDataClustering	0.083	0.049	0.039
getDataForOneOma	0.001	0.001	0.001
getDendrogram	0.305	0.210	0.117
getDistanceMatrix	0.095	0.065	0.033
getDomainFolder	0.001	0.001	0.001
getFastaFromFasInput	0.090	0.055	0.035
getFastaFromFile	0.069	0.047	0.024
getFastaFromFolder	0.033	0.021	0.014
getIDsRank	0.154	0.105	0.057
getInputTaxaID	0.010	0.013	0.006
getInputTaxaName	0.062	0.049	0.025
getNameList	0.255	0.206	0.103
getOmaDataForOneOrtholog	0.002	0.001	0.001
getOmaDomainFromURL	0.002	0.001	0.000
getOmaMembers	0.001	0.001	0.001
getQualColForVector	0.002	0.001	0.001
getSelectedFastaOma	0.002	0.002	0.001
getSelectedTaxonNames	0.066	0.046	0.041
getTaxonomyInfo	0.017	0.002	0.019
getTaxonomyMatrix	0.145	0.080	0.226
getTaxonomyRanks	0.001	0.001	0.001
gridArrangeSharedLegend	1.025	0.010	1.035
heatmapPlotting	1.157	0.354	0.827
highlightProfilePlot	1.324	0.336	1.000
mainTaxonomyRank	0.001	0.000	0.001
pairDomainPlotting	0.000	0.001	0.001
parseDomainInput	0.036	0.015	0.051
parseInfoProfile	0.221	0.049	0.271
processNcbiTaxonomy	0.139	0.062	0.239
qualitativeColours	0.001	0.001	0.000
rankIndexing	0.000	0.000	0.001
reduceProfile	0.034	0.009	0.044
runPhyloprofile	0.127	0.043	0.171
singleDomainPlotting	0.001	0.001	0.001
sortDomains	0.000	0.001	0.001
sortInputTaxa	0.109	0.027	0.137
sortTaxaFromTree	0.025	0.001	0.027
taxonomyTableCreator	0.577	0.362	0.250
varDistTaxPlot	2.158	0.389	1.910
wideToLong	0.029	0.009	0.038
xmlParser	0.078	0.014	0.094