Multiple platform build/check report for BioC 3.10 - CHECK report for PhyloProfile on merida1

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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_1.0.7.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/PhyloProfile.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.0.7’
* 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

Installation output

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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/3.6/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


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 10.352   3.020   9.194

Example timings

name	user	system	elapsed
calcPresSpec	0.325	0.005	0.330
checkInputValidity	0.010	0.000	0.011
checkNewick	0.003	0.000	0.003
checkOmaID	0.001	0.000	0.000
clusterDataDend	0.132	0.177	0.048
compareMedianTaxonGroups	0.164	0.250	0.053
compareTaxonGroups	0.243	0.364	0.083
createArchiPlot	0.864	0.185	0.782
createGeneAgePlot	0.277	0.005	0.288
createLongMatrix	0.053	0.007	0.060
createPercentageDistributionData	0.158	0.086	0.245
createProfileFromOma	0.001	0.000	0.001
createRootedTree	0.023	0.001	0.024
createVarDistPlot	0.258	0.010	0.269
createVariableDistributionData	0.018	0.012	0.029
createVariableDistributionDataSubset	0.014	0.015	0.030
dataCustomizedPlot	0.224	0.355	0.084
dataFeatureTaxGroup	0.098	0.186	0.036
dataMainPlot	0.339	0.591	0.118
dataVarDistTaxGroup	0.054	0.111	0.020
estimateGeneAge	0.229	0.417	0.089
fastaParser	0.040	0.000	0.043
featureDistTaxPlot	0.259	0.009	0.270
filterProfileData	0.026	0.012	0.037
fromInputToProfile	0.175	0.050	0.226
geneAgePlotDf	0.005	0.000	0.004
generateSinglePlot	0.475	0.010	0.488
getAllDomainsOma	0.000	0.000	0.054
getAllFastaOma	0	0	0
getCommonAncestor	0.059	0.012	0.071
getCoreGene	0.015	0.014	0.029
getDataClustering	0.076	0.074	0.039
getDataForOneOma	0.001	0.001	0.000
getDendrogram	0.257	0.255	0.089
getDistanceMatrix	0.106	0.134	0.035
getDomainFolder	0.001	0.002	0.000
getFastaFromFasInput	0.083	0.098	0.026
getFastaFromFile	0.062	0.064	0.018
getFastaFromFolder	0.043	0.045	0.012
getIDsRank	0.136	0.170	0.044
getInputTaxaID	0.033	0.066	0.014
getInputTaxaName	0.113	0.205	0.042
getNameList	0.284	0.451	0.095
getOmaDataForOneOrtholog	0.001	0.002	0.000
getOmaDomainFromURL	0.002	0.002	0.001
getOmaMembers	0.001	0.002	0.000
getQualColForVector	0.002	0.003	0.001
getSelectedFastaOma	0.001	0.003	0.001
getSelectedTaxonNames	0.066	0.090	0.060
getTaxonomyInfo	0.014	0.001	0.015
getTaxonomyMatrix	0.234	0.073	0.314
getTaxonomyRanks	0.000	0.000	0.001
gridArrangeSharedLegend	0.860	0.014	0.880
heatmapPlotting	1.038	0.737	0.599
highlightProfilePlot	1.335	0.922	0.911
mainTaxonomyRank	0.000	0.001	0.001
pairDomainPlotting	0	0	0
parseDomainInput	0.040	0.009	0.049
parseInfoProfile	0.179	0.085	0.264
processNcbiTaxonomy	0.088	0.026	0.126
qualitativeColours	0.000	0.000	0.001
rankIndexing	0	0	0
reduceProfile	0.027	0.013	0.042
runPhyloprofile	0.091	0.019	0.111
singleDomainPlotting	0.001	0.000	0.001
sortDomains	0.001	0.000	0.000
sortInputTaxa	0.095	0.042	0.139
sortTaxaFromTree	0.013	0.001	0.014
taxonomyTableCreator	0.938	0.454	0.215
varDistTaxPlot	2.458	0.163	1.047
wideToLong	0.025	0.004	0.028
xmlParser	0.080	0.074	0.039

CHECK report for PhyloProfile on merida1

Summary

Command output

Installation output

Tests output

Example timings