Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:07 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 1547/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
PhyloProfile 1.20.4 (landing page) Vinh Tran
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the PhyloProfile package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/PhyloProfile.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: PhyloProfile |
Version: 1.20.4 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PhyloProfile.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PhyloProfile_1.20.4.tar.gz |
StartedAt: 2024-12-21 04:47:39 -0500 (Sat, 21 Dec 2024) |
EndedAt: 2024-12-21 04:51:06 -0500 (Sat, 21 Dec 2024) |
EllapsedTime: 206.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: PhyloProfile.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PhyloProfile.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PhyloProfile_1.20.4.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/PhyloProfile.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘PhyloProfile/DESCRIPTION’ ... OK * this is package ‘PhyloProfile’ version ‘1.20.4’ * 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 code 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 ... 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/Resources/bin/R CMD INSTALL PhyloProfile ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/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 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 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") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 20 ] > > proc.time() user system elapsed 8.841 0.521 9.375
PhyloProfile.Rcheck/PhyloProfile-Ex.timings
name | user | system | elapsed | |
addDimRedTaxaColors | 1.425 | 0.049 | 1.477 | |
addFeatureColors | 0.032 | 0.002 | 0.035 | |
addRankDivisionPlot | 0.700 | 0.019 | 0.720 | |
calcPresSpec | 0.057 | 0.002 | 0.059 | |
checkColorPalette | 0 | 0 | 0 | |
checkInputValidity | 0.004 | 0.001 | 0.006 | |
checkNewick | 0.003 | 0.000 | 0.003 | |
checkOmaID | 0 | 0 | 0 | |
checkOverlapDomains | 0.016 | 0.001 | 0.018 | |
clusterDataDend | 0.018 | 0.002 | 0.020 | |
compareMedianTaxonGroups | 0.026 | 0.003 | 0.029 | |
compareTaxonGroups | 0.033 | 0.003 | 0.037 | |
createArchiPlot | 2.608 | 0.025 | 2.633 | |
createDimRedPlotData | 0.632 | 0.017 | 0.649 | |
createGeneAgePlot | 0.202 | 0.003 | 0.205 | |
createLongMatrix | 0.017 | 0.007 | 0.024 | |
createPercentageDistributionData | 0.094 | 0.014 | 0.109 | |
createProfileFromOma | 0 | 0 | 0 | |
createUnrootedTree | 0.013 | 0.001 | 0.014 | |
createVarDistPlot | 0.137 | 0.003 | 0.140 | |
createVariableDistributionData | 0.009 | 0.003 | 0.012 | |
createVariableDistributionDataSubset | 0.008 | 0.001 | 0.010 | |
dataCustomizedPlot | 0.016 | 0.001 | 0.018 | |
dataFeatureTaxGroup | 0.014 | 0.002 | 0.016 | |
dataMainPlot | 0.024 | 0.008 | 0.032 | |
dataVarDistTaxGroup | 0.006 | 0.002 | 0.007 | |
dimReduction | 0.623 | 0.010 | 0.633 | |
estimateGeneAge | 0.128 | 0.014 | 0.143 | |
fastaParser | 0.034 | 0.001 | 0.036 | |
featureDistTaxPlot | 0.182 | 0.003 | 0.185 | |
filterProfileData | 0.125 | 0.026 | 0.151 | |
fromInputToProfile | 0.097 | 0.012 | 0.110 | |
geneAgePlotDf | 0.008 | 0.000 | 0.009 | |
generateSinglePlot | 0.366 | 0.009 | 0.375 | |
getAllDomainsOma | 0 | 0 | 0 | |
getAllFastaOma | 0 | 0 | 0 | |
getCommonAncestor | 0.031 | 0.004 | 0.035 | |
getCoreGene | 0.104 | 0.013 | 0.117 | |
getDataClustering | 0.016 | 0.002 | 0.018 | |
getDataForOneOma | 0 | 0 | 0 | |
getDendrogram | 0.047 | 0.003 | 0.050 | |
getDistanceMatrix | 0.016 | 0.001 | 0.018 | |
getDomainFolder | 0.001 | 0.001 | 0.001 | |
getFastaFromFasInput | 0.016 | 0.001 | 0.016 | |
getFastaFromFile | 0.010 | 0.002 | 0.012 | |
getFastaFromFolder | 0.007 | 0.001 | 0.009 | |
getIDsRank | 0.018 | 0.002 | 0.019 | |
getInputTaxaID | 0.002 | 0.001 | 0.004 | |
getInputTaxaName | 0.012 | 0.003 | 0.015 | |
getNameList | 0.023 | 0.019 | 0.042 | |
getOmaDataForOneOrtholog | 0 | 0 | 0 | |
getOmaDomainFromURL | 0 | 0 | 0 | |
getOmaMembers | 0 | 0 | 0 | |
getQualColForVector | 0.001 | 0.000 | 0.001 | |
getSelectedFastaOma | 0.000 | 0.001 | 0.001 | |
getSelectedTaxonNames | 0.020 | 0.005 | 0.024 | |
getTaxHierarchy | 0.014 | 0.001 | 0.015 | |
getTaxonomyInfo | 0.012 | 0.001 | 0.014 | |
getTaxonomyMatrix | 0.097 | 0.073 | 0.170 | |
getTaxonomyRanks | 0.001 | 0.001 | 0.000 | |
gridArrangeSharedLegend | 0 | 0 | 0 | |
groupLabelDimRedData | 0.052 | 0.007 | 0.057 | |
heatmapPlotting | 0.268 | 0.004 | 0.272 | |
heatmapPlottingFast | 4.328 | 0.149 | 4.289 | |
highlightProfilePlot | 0.299 | 0.006 | 0.305 | |
id2name | 0.005 | 0.001 | 0.006 | |
joinPlotMergeLegends | 0.536 | 0.032 | 0.569 | |
linearizeArchitecture | 0.008 | 0.000 | 0.009 | |
mainTaxonomyRank | 0.000 | 0.000 | 0.001 | |
modifyFeatureName | 0.020 | 0.013 | 0.033 | |
pairDomainPlotting | 0.401 | 0.003 | 0.405 | |
parseDomainInput | 0.020 | 0.012 | 0.032 | |
parseInfoProfile | 0.082 | 0.021 | 0.103 | |
plotDimRed | 0.923 | 0.015 | 0.938 | |
plotDimRed3D | 0.929 | 0.027 | 0.957 | |
prepareDimRedData | 0.053 | 0.006 | 0.060 | |
processNcbiTaxonomy | 0.000 | 0.000 | 0.001 | |
processOrthoID | 0.131 | 0.063 | 0.224 | |
qualitativeColours | 0.000 | 0.001 | 0.001 | |
rankIndexing | 0.065 | 0.002 | 0.068 | |
reduceProfile | 0.014 | 0.006 | 0.020 | |
resolveOverlapFeatures | 0.015 | 0.001 | 0.017 | |
runPhyloProfile | 0 | 0 | 0 | |
singleDomainPlotting | 0.174 | 0.003 | 0.176 | |
sortDomains | 0.008 | 0.001 | 0.009 | |
sortDomainsByList | 0.010 | 0.001 | 0.011 | |
sortInputTaxa | 0.031 | 0.007 | 0.038 | |
sortTaxaFromTree | 0.011 | 0.001 | 0.012 | |
taxonomyTableCreator | 0.085 | 0.004 | 0.089 | |
varDistTaxPlot | 0.757 | 0.009 | 0.765 | |
wideToLong | 0.013 | 0.006 | 0.019 | |
xmlParser | 0.016 | 0.003 | 0.019 | |