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This page was generated on 2021-10-15 15:06:46 -0400 (Fri, 15 Oct 2021).

CHECK results for PhyloProfile on machv2

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? here 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 1388/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PhyloProfile 1.6.6  (landing page)
Vinh Tran
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/PhyloProfile
git_branch: RELEASE_3_13
git_last_commit: 92e2e9e
git_last_commit_date: 2021-06-29 05:53:37 -0400 (Tue, 29 Jun 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: PhyloProfile
Version: 1.6.6
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:PhyloProfile.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings PhyloProfile_1.6.6.tar.gz
StartedAt: 2021-10-14 22:19:27 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 22:22:47 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 199.9 seconds
RetCode: 0
Status:   OK  
CheckDir: PhyloProfile.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:PhyloProfile.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings PhyloProfile_1.6.6.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/PhyloProfile.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PhyloProfile/DESCRIPTION’ ... OK
* this is package ‘PhyloProfile’ version ‘1.6.6’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/PhyloProfile.Rcheck/00check.log’
for details.



Installation output

PhyloProfile.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 
  9.632   0.577  10.195 

Example timings

PhyloProfile.Rcheck/PhyloProfile-Ex.timings

nameusersystemelapsed
calcPresSpec0.0370.0030.040
checkInputValidity0.0150.0010.018
checkNewick0.0040.0010.005
checkOmaID0.0000.0010.000
clusterDataDend0.0370.0020.038
compareMedianTaxonGroups0.0460.0030.049
compareTaxonGroups0.0590.0030.063
createArchiPlot0.7160.0080.724
createGeneAgePlot0.2280.0030.230
createLongMatrix0.0380.0130.052
createPercentageDistributionData0.5570.0230.579
createProfileFromOma0.0000.0010.001
createRootedTree0.0230.0020.024
createVarDistPlot0.1820.0060.187
createVariableDistributionData0.0070.0040.012
createVariableDistributionDataSubset0.0130.0020.016
dataCustomizedPlot0.0170.0030.020
dataFeatureTaxGroup0.0220.0010.024
dataMainPlot0.020.010.03
dataVarDistTaxGroup0.0090.0020.012
estimateGeneAge0.1440.0220.167
fastaParser0.0700.0020.072
featureDistTaxPlot0.1920.0100.201
filterProfileData0.2050.0730.279
fromInputToProfile0.1480.0280.177
geneAgePlotDf0.0040.0010.004
generateSinglePlot0.5130.0150.529
getAllDomainsOma0.0000.0000.001
getAllFastaOma000
getCommonAncestor0.0680.0120.080
getCoreGene0.1650.0360.202
getDataClustering0.0170.0020.019
getDataForOneOma000
getDendrogram0.0680.0030.071
getDistanceMatrix0.0180.0010.019
getDomainFolder000
getFastaFromFasInput0.0210.0010.023
getFastaFromFile0.0150.0010.016
getFastaFromFolder0.0100.0010.011
getIDsRank0.0370.0040.041
getInputTaxaID0.0030.0010.004
getInputTaxaName0.0140.0020.015
getNameList0.0380.0410.079
getOmaDataForOneOrtholog000
getOmaDomainFromURL0.0000.0010.000
getOmaMembers0.0000.0000.001
getQualColForVector000
getSelectedFastaOma0.0000.0010.000
getSelectedTaxonNames0.0280.0050.033
getTaxonomyInfo0.0220.0010.023
getTaxonomyMatrix0.1680.1330.302
getTaxonomyRanks0.0010.0000.001
gridArrangeSharedLegend0.6470.0070.654
heatmapPlotting0.2360.0090.245
highlightProfilePlot0.2330.0030.237
mainTaxonomyRank0.0000.0000.001
pairDomainPlotting0.0000.0010.001
parseDomainInput0.0220.0200.041
parseInfoProfile0.1630.0400.202
processNcbiTaxonomy0.1210.0460.190
qualitativeColours000
rankIndexing000
reduceProfile0.0190.0100.029
runPhyloProfile0.1010.0290.133
singleDomainPlotting0.0010.0010.001
sortDomains0.0010.0010.000
sortInputTaxa0.0860.0150.101
sortTaxaFromTree0.0170.0010.018
taxonomyTableCreator0.1630.0050.169
varDistTaxPlot1.1160.0111.128
wideToLong0.0170.0100.026
xmlParser0.0270.0030.032