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This page was generated on 2023-12-05 11:36:59 -0500 (Tue, 05 Dec 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.2 LTS)x86_644.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" 4688
palomino4Windows Server 2022 Datacenterx644.3.2 (2023-10-31 ucrt) -- "Eye Holes" 4421
lconwaymacOS 12.7.1 Montereyx86_644.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" 4440
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 1.16.0  (landing page)
Vinh Tran
Snapshot Date: 2023-12-04 14:05:07 -0500 (Mon, 04 Dec 2023)
git_url: https://git.bioconductor.org/packages/PhyloProfile
git_branch: RELEASE_3_18
git_last_commit: ec26674
git_last_commit_date: 2023-10-24 11:15:33 -0500 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.2 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 palomino4


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: 1.16.0
Command: F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:PhyloProfile.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings PhyloProfile_1.16.0.tar.gz
StartedAt: 2023-12-05 04:33:40 -0500 (Tue, 05 Dec 2023)
EndedAt: 2023-12-05 04:36:16 -0500 (Tue, 05 Dec 2023)
EllapsedTime: 155.9 seconds
RetCode: 0
Status:   OK  
CheckDir: PhyloProfile.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:PhyloProfile.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings PhyloProfile_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.18-bioc/meat/PhyloProfile.Rcheck'
* using R version 4.3.2 (2023-10-31 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.3.0
    GNU Fortran (GCC) 12.3.0
* 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 '1.16.0'
* 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 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:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL PhyloProfile
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.18-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)

Tests output

PhyloProfile.Rcheck/tests/testthat.Rout


R version 4.3.2 (2023-10-31 ucrt) -- "Eye Holes"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 
   7.60    0.59    8.20 

Example timings

PhyloProfile.Rcheck/PhyloProfile-Ex.timings

nameusersystemelapsed
addRankDivisionPlot1.380.041.41
calcPresSpec0.030.000.03
checkInputValidity0.000.010.01
checkNewick0.010.000.02
checkOmaID000
clusterDataDend0.030.000.03
compareMedianTaxonGroups0.050.000.05
compareTaxonGroups0.050.020.06
createArchiPlot0.590.080.67
createGeneAgePlot0.240.000.23
createLongMatrix0.010.010.04
createPercentageDistributionData0.060.020.07
createProfileFromOma000
createUnrootedTree0.020.000.02
createVarDistPlot0.120.000.12
createVariableDistributionData0.020.000.02
createVariableDistributionDataSubset000
dataCustomizedPlot0.020.000.01
dataFeatureTaxGroup0.010.000.02
dataMainPlot0.030.000.03
dataVarDistTaxGroup0.020.000.01
estimateGeneAge0.060.030.10
fastaParser0.020.020.03
featureDistTaxPlot0.180.000.21
filterProfileData0.080.020.09
fromInputToProfile0.110.000.11
geneAgePlotDf000
generateSinglePlot0.620.000.62
getAllDomainsOma000
getAllFastaOma000
getCommonAncestor0.050.000.05
getCoreGene0.050.030.08
getDataClustering0.010.000.01
getDataForOneOma000
getDendrogram0.050.000.05
getDistanceMatrix0.010.000.01
getDomainFolder000
getFastaFromFasInput0.020.000.02
getFastaFromFile0.010.000.02
getFastaFromFolder000
getIDsRank0.050.000.04
getInputTaxaID000
getInputTaxaName0.020.020.03
getNameList0.040.010.07
getOmaDataForOneOrtholog000
getOmaDomainFromURL000
getOmaMembers000
getQualColForVector000
getSelectedFastaOma000
getSelectedTaxonNames0.020.010.03
getTaxHierarchy0.020.000.03
getTaxonomyInfo0.010.000.02
getTaxonomyMatrix0.220.030.25
getTaxonomyRanks000
gridArrangeSharedLegend0.520.020.53
heatmapPlotting0.290.010.31
highlightProfilePlot0.880.000.87
id2name000
mainTaxonomyRank000
modifyFeatureName000
pairDomainPlotting000
parseDomainInput0.050.000.05
parseInfoProfile0.050.080.12
processNcbiTaxonomy0.200.051.06
processOrthoID0.110.040.18
qualitativeColours000
rankIndexing000
reduceProfile0.010.020.03
runPhyloProfile0.110.030.15
singleDomainPlotting000
sortDomains000
sortInputTaxa0.000.050.05
sortTaxaFromTree0.000.010.02
taxonomyTableCreator0.110.020.12
varDistTaxPlot0.890.000.89
wideToLong0.020.000.02
xmlParser0.020.000.02