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This page was generated on 2024-12-23 12:06 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (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 1547/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PhyloProfile 1.20.4  (landing page)
Vinh Tran
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/PhyloProfile
git_branch: RELEASE_3_20
git_last_commit: 44345df
git_last_commit_date: 2024-12-02 05:25:10 -0500 (Mon, 02 Dec 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for PhyloProfile on merida1

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.

raw results


Summary

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: 2024-12-20 07:37:46 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 07:44:25 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 399.4 seconds
RetCode: 0
Status:   OK  
CheckDir: PhyloProfile.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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: x86_64-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 Monterey 12.7.6
* 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
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
createArchiPlot 5.231  0.051   5.342
* 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


Installation output

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-x86_64/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

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: x86_64-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 
 16.312   1.032  17.503 

Example timings

PhyloProfile.Rcheck/PhyloProfile-Ex.timings

nameusersystemelapsed
addDimRedTaxaColors2.0080.1402.162
addFeatureColors0.0580.0040.067
addRankDivisionPlot1.6480.0351.703
calcPresSpec0.1040.0040.116
checkColorPalette0.0010.0000.002
checkInputValidity0.0070.0020.009
checkNewick0.0040.0010.005
checkOmaID000
checkOverlapDomains0.0290.0010.031
clusterDataDend0.0410.0030.044
compareMedianTaxonGroups0.0610.0060.067
compareTaxonGroups0.0820.0060.092
createArchiPlot5.2310.0515.342
createDimRedPlotData1.3150.0361.363
createGeneAgePlot0.4440.0040.455
createLongMatrix0.0320.0210.053
createPercentageDistributionData0.1960.0250.222
createProfileFromOma0.0000.0010.000
createUnrootedTree0.0340.0020.036
createVarDistPlot0.3710.0040.377
createVariableDistributionData0.0140.0090.023
createVariableDistributionDataSubset0.0140.0030.017
dataCustomizedPlot0.0390.0050.043
dataFeatureTaxGroup0.0280.0040.031
dataMainPlot0.0500.0220.072
dataVarDistTaxGroup0.0090.0030.013
dimReduction1.8450.0221.885
estimateGeneAge0.2760.0220.303
fastaParser0.0670.0030.070
featureDistTaxPlot0.4530.0050.467
filterProfileData0.2390.0720.323
fromInputToProfile0.2160.0310.248
geneAgePlotDf0.0160.0010.017
generateSinglePlot0.8340.0080.845
getAllDomainsOma0.0000.0010.000
getAllFastaOma0.0010.0010.000
getCommonAncestor0.1050.0090.114
getCoreGene0.1890.0170.208
getDataClustering0.0350.0050.040
getDataForOneOma0.0000.0010.001
getDendrogram0.1050.0060.115
getDistanceMatrix0.0370.0020.040
getDomainFolder0.0010.0010.001
getFastaFromFasInput0.0320.0010.034
getFastaFromFile0.0210.0020.025
getFastaFromFolder0.0150.0020.018
getIDsRank0.0440.0050.050
getInputTaxaID0.0050.0030.006
getInputTaxaName0.0230.0050.030
getNameList0.0440.0660.111
getOmaDataForOneOrtholog000
getOmaDomainFromURL0.0010.0010.001
getOmaMembers0.0000.0010.000
getQualColForVector0.0010.0010.001
getSelectedFastaOma000
getSelectedTaxonNames0.0370.0080.045
getTaxHierarchy0.0320.0040.038
getTaxonomyInfo0.0290.0040.032
getTaxonomyMatrix0.2320.2570.496
getTaxonomyRanks0.0000.0010.001
gridArrangeSharedLegend0.0000.0010.002
groupLabelDimRedData0.0980.0120.110
heatmapPlotting0.6180.0100.631
heatmapPlottingFast4.5790.2614.561
highlightProfilePlot0.6720.0130.688
id2name0.0080.0020.010
joinPlotMergeLegends1.3550.0551.459
linearizeArchitecture0.0180.0020.020
mainTaxonomyRank0.0000.0010.002
modifyFeatureName0.0390.0570.101
pairDomainPlotting0.9980.0091.053
parseDomainInput0.0340.0410.076
parseInfoProfile0.1530.0560.211
plotDimRed1.9410.0262.037
plotDimRed3D1.8560.0861.950
prepareDimRedData0.0990.0130.111
processNcbiTaxonomy0.0010.0010.001
processOrthoID0.2170.1010.344
qualitativeColours0.0010.0000.001
rankIndexing0.1410.0060.148
reduceProfile0.0290.0180.047
resolveOverlapFeatures0.0360.0020.039
runPhyloProfile0.0000.0000.001
singleDomainPlotting0.4080.0050.416
sortDomains0.0160.0030.019
sortDomainsByList0.0180.0020.021
sortInputTaxa0.0680.0120.079
sortTaxaFromTree0.0320.0020.034
taxonomyTableCreator0.2250.0090.235
varDistTaxPlot1.8140.0141.834
wideToLong0.0230.0230.052
xmlParser0.0360.0080.045