Back to Multiple platform build/check report for BioC 3.15
ABCDEFGHIJKLMNO[P]QRSTUVWXYZ

This page was generated on 2022-05-20 12:05:43 -0400 (Fri, 20 May 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4380
palomino3Windows Server 2022 Datacenterx644.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" 4155
merida1macOS 10.14.6 Mojavex86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4221
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

CHECK results for PhyloProfile on nebbiolo1


To the developers/maintainers of the PhyloProfile package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1452/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PhyloProfile 1.10.1  (landing page)
Vinh Tran
Snapshot Date: 2022-05-19 13:55:15 -0400 (Thu, 19 May 2022)
git_url: https://git.bioconductor.org/packages/PhyloProfile
git_branch: RELEASE_3_15
git_last_commit: bbf42d9
git_last_commit_date: 2022-04-29 05:56:42 -0400 (Fri, 29 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 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 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: PhyloProfile
Version: 1.10.1
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:PhyloProfile.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings PhyloProfile_1.10.1.tar.gz
StartedAt: 2022-05-19 20:52:27 -0400 (Thu, 19 May 2022)
EndedAt: 2022-05-19 20:54:42 -0400 (Thu, 19 May 2022)
EllapsedTime: 135.1 seconds
RetCode: 0
Status:   OK  
CheckDir: PhyloProfile.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:PhyloProfile.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings PhyloProfile_1.10.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/PhyloProfile.Rcheck’
* using R version 4.2.0 (2022-04-22)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PhyloProfile/DESCRIPTION’ ... OK
* this is package ‘PhyloProfile’ version ‘1.10.1’
* 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:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL PhyloProfile
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-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 4.2.0 (2022-04-22) -- "Vigorous Calisthenics"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 
  6.866   0.560   7.413 

Example timings

PhyloProfile.Rcheck/PhyloProfile-Ex.timings

nameusersystemelapsed
calcPresSpec0.0320.0000.031
checkInputValidity0.0040.0040.009
checkNewick0.0020.0000.003
checkOmaID000
clusterDataDend0.0310.0000.030
compareMedianTaxonGroups0.0290.0000.028
compareTaxonGroups0.0320.0040.036
createArchiPlot1.0470.0721.119
createGeneAgePlot0.1240.0240.148
createLongMatrix0.0170.0080.025
createPercentageDistributionData0.0800.0160.096
createProfileFromOma000
createRootedTree0.010.000.01
createVarDistPlot0.130.000.13
createVariableDistributionData0.0060.0040.010
createVariableDistributionDataSubset0.0080.0000.008
dataCustomizedPlot0.010.000.01
dataFeatureTaxGroup0.0120.0000.012
dataMainPlot0.0090.0080.017
dataVarDistTaxGroup0.0020.0040.006
estimateGeneAge0.1100.0080.118
fastaParser0.0370.0000.037
featureDistTaxPlot0.1540.0000.153
filterProfileData0.0970.0320.128
fromInputToProfile0.0960.0120.108
geneAgePlotDf0.0030.0000.004
generateSinglePlot0.2880.0000.288
getAllDomainsOma0.0010.0000.000
getAllFastaOma0.0010.0000.000
getCommonAncestor0.0300.0040.033
getCoreGene0.0910.0200.111
getDataClustering0.0110.0000.011
getDataForOneOma0.0000.0000.001
getDendrogram0.0410.0040.046
getDistanceMatrix0.0120.0000.013
getDomainFolder000
getFastaFromFasInput0.0150.0000.015
getFastaFromFile0.0090.0000.009
getFastaFromFolder0.0120.0000.012
getIDsRank0.0250.0000.025
getInputTaxaID0.0030.0000.003
getInputTaxaName0.0070.0040.009
getNameList0.0170.0360.053
getOmaDataForOneOrtholog000
getOmaDomainFromURL000
getOmaMembers0.0010.0000.000
getQualColForVector0.0010.0000.001
getSelectedFastaOma0.0010.0000.001
getSelectedTaxonNames0.0160.0000.016
getTaxonomyInfo0.0120.0000.012
getTaxonomyMatrix0.0690.1200.189
getTaxonomyRanks0.0010.0000.001
gridArrangeSharedLegend0.4440.0080.452
heatmapPlotting0.1920.0000.193
highlightProfilePlot0.1960.0240.220
mainTaxonomyRank0.0010.0000.001
pairDomainPlotting0.0010.0000.000
parseDomainInput0.0160.0080.024
parseInfoProfile0.5890.0400.629
processNcbiTaxonomy0.0880.0130.110
qualitativeColours0.0000.0000.001
rankIndexing000
reduceProfile0.0080.0080.016
runPhyloProfile0.0670.0080.075
singleDomainPlotting0.0000.0000.001
sortDomains0.0000.0000.001
sortInputTaxa0.0530.0040.057
sortTaxaFromTree0.010.000.01
taxonomyTableCreator0.10.00.1
varDistTaxPlot0.5460.0240.570
wideToLong0.0110.0080.019
xmlParser0.0210.0000.021