Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-21 11:41 -0400 (Wed, 21 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4414 |
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 1527/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
PhyloProfile 1.19.7 (landing page) Vinh Tran
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | 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: 1.19.7 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:PhyloProfile.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings PhyloProfile_1.19.7.tar.gz |
StartedAt: 2024-08-21 03:47:03 -0400 (Wed, 21 Aug 2024) |
EndedAt: 2024-08-21 03:50:59 -0400 (Wed, 21 Aug 2024) |
EllapsedTime: 236.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: PhyloProfile.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:PhyloProfile.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings PhyloProfile_1.19.7.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/PhyloProfile.Rcheck' * using R version 4.4.1 (2024-06-14 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'PhyloProfile/DESCRIPTION' ... OK * this is package 'PhyloProfile' version '1.19.7' * 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 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: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL PhyloProfile ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-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)
PhyloProfile.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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 9.40 0.98 10.42
PhyloProfile.Rcheck/PhyloProfile-Ex.timings
name | user | system | elapsed | |
addFeatureColors | 0.05 | 0.00 | 0.06 | |
addRankDivisionPlot | 1.53 | 0.10 | 1.66 | |
calcPresSpec | 0.05 | 0.00 | 0.04 | |
checkColorPallete | 0 | 0 | 0 | |
checkInputValidity | 0.01 | 0.00 | 0.04 | |
checkNewick | 0 | 0 | 0 | |
checkOmaID | 0 | 0 | 0 | |
checkOverlapDomains | 0.02 | 0.00 | 0.02 | |
clusterDataDend | 0.01 | 0.00 | 0.02 | |
compareMedianTaxonGroups | 0.02 | 0.02 | 0.03 | |
compareTaxonGroups | 0.03 | 0.01 | 0.05 | |
createArchiPlot | 2.87 | 0.02 | 2.89 | |
createGeneAgePlot | 0.28 | 0.00 | 0.28 | |
createLongMatrix | 0.03 | 0.02 | 0.05 | |
createPercentageDistributionData | 0.09 | 0.03 | 0.13 | |
createProfileFromOma | 0 | 0 | 0 | |
createUmapPlotData | 0.97 | 0.04 | 1.03 | |
createUnrootedTree | 0.01 | 0.00 | 0.02 | |
createVarDistPlot | 0.13 | 0.02 | 0.14 | |
createVariableDistributionData | 0.02 | 0.00 | 0.01 | |
createVariableDistributionDataSubset | 0.01 | 0.00 | 0.02 | |
dataCustomizedPlot | 0.02 | 0.00 | 0.01 | |
dataFeatureTaxGroup | 0.01 | 0.00 | 0.01 | |
dataMainPlot | 0.03 | 0.02 | 0.05 | |
dataVarDistTaxGroup | 0.02 | 0.00 | 0.01 | |
estimateGeneAge | 0.17 | 0.02 | 0.19 | |
fastaParser | 0.05 | 0.00 | 0.06 | |
featureDistTaxPlot | 0.31 | 0.00 | 0.32 | |
filterProfileData | 0.11 | 0.04 | 0.15 | |
fromInputToProfile | 0.14 | 0.02 | 0.16 | |
geneAgePlotDf | 0.02 | 0.00 | 0.02 | |
generateSinglePlot | 0.65 | 0.01 | 0.67 | |
getAllDomainsOma | 0 | 0 | 0 | |
getAllFastaOma | 0 | 0 | 0 | |
getCommonAncestor | 0.61 | 0.02 | 0.62 | |
getCoreGene | 0.14 | 0.03 | 0.17 | |
getDataClustering | 0.02 | 0.00 | 0.02 | |
getDataForOneOma | 0 | 0 | 0 | |
getDendrogram | 0.05 | 0.00 | 0.04 | |
getDistanceMatrix | 0.02 | 0.00 | 0.01 | |
getDomainFolder | 0 | 0 | 0 | |
getFastaFromFasInput | 0.01 | 0.00 | 0.02 | |
getFastaFromFile | 0.03 | 0.00 | 0.05 | |
getFastaFromFolder | 0.00 | 0.00 | 0.03 | |
getIDsRank | 0.03 | 0.01 | 0.06 | |
getInputTaxaID | 0 | 0 | 0 | |
getInputTaxaName | 0.00 | 0.01 | 0.01 | |
getNameList | 0.07 | 0.00 | 0.06 | |
getOmaDataForOneOrtholog | 0 | 0 | 0 | |
getOmaDomainFromURL | 0 | 0 | 0 | |
getOmaMembers | 0 | 0 | 0 | |
getQualColForVector | 0 | 0 | 0 | |
getSelectedFastaOma | 0 | 0 | 0 | |
getSelectedTaxonNames | 0.01 | 0.01 | 0.03 | |
getTaxHierarchy | 0.03 | 0.00 | 0.03 | |
getTaxonomyInfo | 0.03 | 0.00 | 0.03 | |
getTaxonomyMatrix | 0.15 | 0.07 | 0.21 | |
getTaxonomyRanks | 0 | 0 | 0 | |
gridArrangeSharedLegend | 0.96 | 0.00 | 0.96 | |
heatmapPlotting | 0.39 | 0.00 | 0.40 | |
highlightProfilePlot | 0.36 | 0.01 | 0.37 | |
id2name | 0 | 0 | 0 | |
joinPlotMergeLegends | 0.72 | 0.02 | 0.73 | |
linearizeArchitecture | 0.02 | 0.00 | 0.02 | |
mainTaxonomyRank | 0 | 0 | 0 | |
modifyFeatureName | 0.03 | 0.02 | 0.04 | |
pairDomainPlotting | 0.47 | 0.02 | 0.49 | |
parseDomainInput | 0.03 | 0.00 | 0.03 | |
parseInfoProfile | 0.11 | 0.03 | 0.14 | |
plotUmap | 1.16 | 0.01 | 1.17 | |
prepareUmapData | 0.04 | 0.02 | 0.06 | |
processNcbiTaxonomy | 0 | 0 | 0 | |
processOrthoID | 0.24 | 0.06 | 1.18 | |
qualitativeColours | 0 | 0 | 0 | |
rankIndexing | 0.03 | 0.00 | 0.04 | |
reduceProfile | 0.01 | 0.02 | 0.03 | |
resolveOverlapFeatures | 0.02 | 0.00 | 0.02 | |
runPhyloProfile | 0 | 0 | 0 | |
singleDomainPlotting | 0.25 | 0.00 | 0.25 | |
sortDomains | 0.03 | 0.00 | 0.03 | |
sortDomainsByList | 0.02 | 0.00 | 0.02 | |
sortInputTaxa | 0.03 | 0.01 | 0.04 | |
sortTaxaFromTree | 0.01 | 0.00 | 0.02 | |
taxonomyTableCreator | 0.08 | 0.00 | 0.09 | |
umapClustering | 0.75 | 0.03 | 0.78 | |
varDistTaxPlot | 1.06 | 0.02 | 1.08 | |
wideToLong | 0.02 | 0.00 | 0.02 | |
xmlParser | 0.01 | 0.01 | 0.06 | |