Back to Multiple platform build/check report for BioC 3.18:   simplified   long
ABCDEFGHIJKLMNO[P]QRSTUVWXYZ

This page was generated on 2024-03-04 11:37:41 -0500 (Mon, 04 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" 4692
palomino4Windows Server 2022 Datacenterx644.3.2 (2023-10-31 ucrt) -- "Eye Holes" 4445
lconwaymacOS 12.7.1 Montereyx86_644.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" 4466
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 1545/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PhyloProfile 1.16.3  (landing page)
Vinh Tran
Snapshot Date: 2024-03-03 14:05:05 -0500 (Sun, 03 Mar 2024)
git_url: https://git.bioconductor.org/packages/PhyloProfile
git_branch: RELEASE_3_18
git_last_commit: 17dee2d
git_last_commit_date: 2024-02-15 04:34:00 -0500 (Thu, 15 Feb 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for PhyloProfile on lconway


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: 1.16.3
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_1.16.3.tar.gz
StartedAt: 2024-03-03 22:33:36 -0500 (Sun, 03 Mar 2024)
EndedAt: 2024-03-03 22:36:34 -0500 (Sun, 03 Mar 2024)
EllapsedTime: 178.4 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_1.16.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/PhyloProfile.Rcheck’
* using R version 4.3.2 Patched (2023-11-01 r85457)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PhyloProfile/DESCRIPTION’ ... OK
* this is package ‘PhyloProfile’ version ‘1.16.3’
* 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

PhyloProfile.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL PhyloProfile
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-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 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (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")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 20 ]
> 
> proc.time()
   user  system elapsed 
  7.861   0.609   8.543 

Example timings

PhyloProfile.Rcheck/PhyloProfile-Ex.timings

nameusersystemelapsed
addRankDivisionPlot1.3610.0501.423
calcPresSpec0.0270.0070.035
checkInputValidity0.0090.0020.012
checkNewick0.0030.0010.004
checkOmaID0.0000.0000.001
clusterDataDend0.0200.0030.024
compareMedianTaxonGroups0.0250.0050.032
compareTaxonGroups0.0380.0060.045
createArchiPlot0.5380.0410.586
createGeneAgePlot0.2370.0030.243
createLongMatrix0.0250.0090.035
createPercentageDistributionData0.0650.0150.081
createProfileFromOma000
createUnrootedTree0.0130.0010.014
createVarDistPlot0.1480.0030.153
createVariableDistributionData0.0070.0040.011
createVariableDistributionDataSubset0.0090.0030.012
dataCustomizedPlot0.0210.0020.023
dataFeatureTaxGroup0.0150.0020.017
dataMainPlot0.0260.0100.038
dataVarDistTaxGroup0.0060.0030.008
estimateGeneAge0.0880.0120.101
fastaParser0.0430.0030.046
featureDistTaxPlot0.2210.0050.226
filterProfileData0.0710.0250.097
fromInputToProfile0.0750.0120.089
geneAgePlotDf0.0040.0000.005
generateSinglePlot0.6180.0150.638
getAllDomainsOma000
getAllFastaOma000
getCommonAncestor0.0330.0050.038
getCoreGene0.0490.0100.060
getDataClustering0.0110.0020.014
getDataForOneOma0.0000.0000.001
getDendrogram0.0320.0030.034
getDistanceMatrix0.0110.0010.013
getDomainFolder000
getFastaFromFasInput0.0140.0010.014
getFastaFromFile0.0120.0010.013
getFastaFromFolder0.0090.0010.011
getIDsRank0.0270.0030.031
getInputTaxaID0.0020.0010.003
getInputTaxaName0.0110.0030.014
getNameList0.0190.0190.038
getOmaDataForOneOrtholog000
getOmaDomainFromURL0.0000.0000.001
getOmaMembers000
getQualColForVector0.0010.0010.000
getSelectedFastaOma000
getSelectedTaxonNames0.0170.0050.023
getTaxHierarchy0.0180.0020.020
getTaxonomyInfo0.0140.0020.017
getTaxonomyMatrix0.1050.0810.188
getTaxonomyRanks000
gridArrangeSharedLegend1.0710.0221.101
heatmapPlotting0.2970.0040.302
highlightProfilePlot0.3020.0040.308
id2name0.0030.0010.004
mainTaxonomyRank0.0000.0000.001
modifyFeatureName0.0010.0000.000
pairDomainPlotting0.0000.0010.001
parseDomainInput0.0220.0160.038
parseInfoProfile0.0500.0180.068
processNcbiTaxonomy0.1030.0770.257
processOrthoID0.0920.0510.167
qualitativeColours000
rankIndexing0.0000.0000.001
reduceProfile0.0150.0090.029
runPhyloProfile0.1080.0530.190
singleDomainPlotting0.0010.0000.000
sortDomains000
sortInputTaxa0.0340.0080.042
sortTaxaFromTree0.0140.0010.016
taxonomyTableCreator0.1230.0090.134
varDistTaxPlot1.2520.0241.285
wideToLong0.0130.0060.018
xmlParser0.0270.0030.031