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This page was generated on 2024-02-18 02:28:59 -0500 (Sun, 18 Feb 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4657
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" 4397
merida1macOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4424
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" 4400
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 1527/2244HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PhyloProfile 1.17.4  (landing page)
Vinh Tran
Snapshot Date: 2024-02-16 14:10:20 -0500 (Fri, 16 Feb 2024)
git_url: https://git.bioconductor.org/packages/PhyloProfile
git_branch: devel
git_last_commit: bb8955f
git_last_commit_date: 2024-02-15 05:32:13 -0500 (Thu, 15 Feb 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  YES
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

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: 1.17.4
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_1.17.4.tar.gz
StartedAt: 2024-02-17 08:22:03 -0500 (Sat, 17 Feb 2024)
EndedAt: 2024-02-17 08:27:53 -0500 (Sat, 17 Feb 2024)
EllapsedTime: 349.3 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_1.17.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/PhyloProfile.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* 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 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PhyloProfile/DESCRIPTION’ ... OK
* this is package ‘PhyloProfile’ version ‘1.17.4’
* 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 ... NOTE
License stub is invalid DCF.
* 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 ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/PhyloProfile.Rcheck/00check.log’
for details.



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 Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences"
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 
 13.280   0.984  16.963 

Example timings

PhyloProfile.Rcheck/PhyloProfile-Ex.timings

nameusersystemelapsed
addRankDivisionPlot1.8620.1642.407
calcPresSpec0.0460.0110.068
checkInputValidity0.0170.0040.026
checkNewick0.0050.0020.008
checkOmaID0.0000.0000.001
clusterDataDend0.0370.0080.057
compareMedianTaxonGroups0.0580.0120.088
compareTaxonGroups0.0760.0140.104
createArchiPlot1.0800.0641.348
createGeneAgePlot0.4840.0050.584
createLongMatrix0.0460.0190.080
createPercentageDistributionData0.1240.0240.182
createProfileFromOma000
createUnrootedTree0.0320.0020.042
createVarDistPlot0.2970.0070.363
createVariableDistributionData0.0140.0100.028
createVariableDistributionDataSubset0.0130.0030.017
dataCustomizedPlot0.0370.0050.050
dataFeatureTaxGroup0.0300.0040.038
dataMainPlot0.0500.0250.095
dataVarDistTaxGroup0.0100.0050.017
estimateGeneAge0.2180.0210.280
fastaParser0.0790.0050.136
featureDistTaxPlot0.4400.0080.550
filterProfileData0.1550.0680.277
fromInputToProfile0.1660.0310.265
geneAgePlotDf0.0090.0010.010
generateSinglePlot1.0980.0211.309
getAllDomainsOma0.0000.0010.001
getAllFastaOma0.0000.0010.000
getCommonAncestor0.0880.0110.121
getCoreGene0.1100.0170.147
getDataClustering0.0310.0060.044
getDataForOneOma000
getDendrogram0.1000.0060.127
getDistanceMatrix0.0290.0020.036
getDomainFolder000
getFastaFromFasInput0.0340.0020.040
getFastaFromFile0.0210.0020.027
getFastaFromFolder0.0150.0020.022
getIDsRank0.0550.0060.071
getInputTaxaID0.0040.0020.007
getInputTaxaName0.0220.0060.035
getNameList0.0440.0650.124
getOmaDataForOneOrtholog0.0000.0010.001
getOmaDomainFromURL0.0000.0010.001
getOmaMembers0.0010.0010.000
getQualColForVector0.0000.0010.001
getSelectedFastaOma0.0000.0010.001
getSelectedTaxonNames0.0330.0080.048
getTaxHierarchy0.0360.0050.044
getTaxonomyInfo0.0490.0030.062
getTaxonomyMatrix0.2240.2420.534
getTaxonomyRanks0.0000.0010.002
gridArrangeSharedLegend1.2960.0181.499
heatmapPlotting0.7610.0090.869
highlightProfilePlot0.8200.0120.959
id2name0.0080.0020.010
mainTaxonomyRank0.0000.0010.001
modifyFeatureName0.0000.0010.000
pairDomainPlotting0.0010.0010.001
parseDomainInput0.0360.0380.085
parseInfoProfile0.1120.0550.189
processNcbiTaxonomy0.1610.0940.345
processOrthoID0.1430.0560.229
qualitativeColours0.0000.0000.001
rankIndexing0.0000.0000.001
reduceProfile0.0270.0160.047
runPhyloProfile0.1460.0580.231
singleDomainPlotting0.0000.0010.001
sortDomains0.0010.0000.001
sortInputTaxa0.0630.0120.087
sortTaxaFromTree0.0310.0020.037
taxonomyTableCreator0.2550.0140.305
varDistTaxPlot1.7400.0192.082
wideToLong0.0280.0200.061
xmlParser0.0340.0080.050