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This page was generated on 2020-10-17 11:59:12 -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 1308/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
PhyloProfile 1.2.8 Vinh Tran
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | [ OK ] | OK |
Package: PhyloProfile |
Version: 1.2.8 |
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_1.2.8.tar.gz |
StartedAt: 2020-10-17 03:55:10 -0400 (Sat, 17 Oct 2020) |
EndedAt: 2020-10-17 03:58:42 -0400 (Sat, 17 Oct 2020) |
EllapsedTime: 212.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: PhyloProfile.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running 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_1.2.8.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/PhyloProfile.Rcheck’ * using R version 4.0.3 (2020-10-10) * using platform: x86_64-apple-darwin17.0 (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
PhyloProfile.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL PhyloProfile ### ############################################################################## ############################################################################## * 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)
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-apple-darwin17.0 (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 9.614 0.515 10.116
PhyloProfile.Rcheck/PhyloProfile-Ex.timings
name | user | system | elapsed | |
calcPresSpec | 0.048 | 0.004 | 0.052 | |
checkInputValidity | 0.012 | 0.001 | 0.014 | |
checkNewick | 0.004 | 0.001 | 0.005 | |
checkOmaID | 0 | 0 | 0 | |
clusterDataDend | 0.048 | 0.003 | 0.051 | |
compareMedianTaxonGroups | 0.045 | 0.004 | 0.048 | |
compareTaxonGroups | 0.064 | 0.004 | 0.068 | |
createArchiPlot | 0.767 | 0.008 | 0.776 | |
createGeneAgePlot | 0.245 | 0.001 | 0.247 | |
createLongMatrix | 0.052 | 0.014 | 0.066 | |
createPercentageDistributionData | 0.529 | 0.033 | 0.563 | |
createProfileFromOma | 0.000 | 0.000 | 0.001 | |
createRootedTree | 0.027 | 0.001 | 0.028 | |
createVarDistPlot | 0.189 | 0.002 | 0.192 | |
createVariableDistributionData | 0.018 | 0.006 | 0.025 | |
createVariableDistributionDataSubset | 0.017 | 0.003 | 0.020 | |
dataCustomizedPlot | 0.051 | 0.016 | 0.067 | |
dataFeatureTaxGroup | 0.024 | 0.002 | 0.025 | |
dataMainPlot | 0.080 | 0.034 | 0.115 | |
dataVarDistTaxGroup | 0.009 | 0.002 | 0.011 | |
estimateGeneAge | 0.097 | 0.011 | 0.108 | |
fastaParser | 0.068 | 0.005 | 0.073 | |
featureDistTaxPlot | 0.275 | 0.015 | 0.292 | |
filterProfileData | 0.032 | 0.021 | 0.116 | |
fromInputToProfile | 0.206 | 0.039 | 0.246 | |
geneAgePlotDf | 0.008 | 0.000 | 0.008 | |
generateSinglePlot | 0.412 | 0.006 | 0.418 | |
getAllDomainsOma | 0.001 | 0.000 | 0.001 | |
getAllFastaOma | 0.000 | 0.000 | 0.001 | |
getCommonAncestor | 0.074 | 0.012 | 0.086 | |
getCoreGene | 0.016 | 0.002 | 0.018 | |
getDataClustering | 0.028 | 0.005 | 0.033 | |
getDataForOneOma | 0.000 | 0.000 | 0.001 | |
getDendrogram | 0.080 | 0.011 | 0.091 | |
getDistanceMatrix | 0.024 | 0.003 | 0.026 | |
getDomainFolder | 0 | 0 | 0 | |
getFastaFromFasInput | 0.028 | 0.004 | 0.031 | |
getFastaFromFile | 0.017 | 0.002 | 0.020 | |
getFastaFromFolder | 0.012 | 0.001 | 0.014 | |
getIDsRank | 0.047 | 0.008 | 0.056 | |
getInputTaxaID | 0.004 | 0.001 | 0.006 | |
getInputTaxaName | 0.018 | 0.004 | 0.022 | |
getNameList | 0.054 | 0.034 | 0.089 | |
getOmaDataForOneOrtholog | 0 | 0 | 0 | |
getOmaDomainFromURL | 0 | 0 | 0 | |
getOmaMembers | 0.000 | 0.000 | 0.001 | |
getQualColForVector | 0.001 | 0.000 | 0.001 | |
getSelectedFastaOma | 0.000 | 0.001 | 0.001 | |
getSelectedTaxonNames | 0.05 | 0.01 | 0.06 | |
getTaxonomyInfo | 0.013 | 0.002 | 0.014 | |
getTaxonomyMatrix | 0.258 | 0.175 | 0.433 | |
getTaxonomyRanks | 0.001 | 0.001 | 0.001 | |
gridArrangeSharedLegend | 0.791 | 0.018 | 0.809 | |
heatmapPlotting | 0.508 | 0.034 | 0.542 | |
highlightProfilePlot | 0.527 | 0.004 | 0.540 | |
mainTaxonomyRank | 0.000 | 0.001 | 0.002 | |
pairDomainPlotting | 0.000 | 0.001 | 0.001 | |
parseDomainInput | 0.046 | 0.023 | 0.069 | |
parseInfoProfile | 0.215 | 0.060 | 0.275 | |
processNcbiTaxonomy | 0.087 | 0.035 | 0.144 | |
qualitativeColours | 0 | 0 | 0 | |
rankIndexing | 0.000 | 0.001 | 0.000 | |
reduceProfile | 0.028 | 0.011 | 0.039 | |
runPhyloProfile | 0.102 | 0.029 | 0.133 | |
singleDomainPlotting | 0.000 | 0.001 | 0.001 | |
sortDomains | 0.000 | 0.001 | 0.000 | |
sortInputTaxa | 0.125 | 0.028 | 0.152 | |
sortTaxaFromTree | 0.026 | 0.001 | 0.028 | |
taxonomyTableCreator | 0.180 | 0.009 | 0.190 | |
varDistTaxPlot | 0.974 | 0.010 | 0.985 | |
wideToLong | 0.037 | 0.013 | 0.050 | |
xmlParser | 0.029 | 0.002 | 0.031 | |