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This page was generated on 2024-12-24 11:40 -0500 (Tue, 24 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4373
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 1539/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PhyloProfile 1.99.1  (landing page)
Vinh Tran
Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024)
git_url: https://git.bioconductor.org/packages/PhyloProfile
git_branch: devel
git_last_commit: 6a63c13
git_last_commit_date: 2024-12-20 09:56:29 -0500 (Fri, 20 Dec 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows 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
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  


CHECK results for PhyloProfile on nebbiolo1

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: 1.99.1
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:PhyloProfile.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings PhyloProfile_1.99.1.tar.gz
StartedAt: 2024-12-24 00:55:57 -0500 (Tue, 24 Dec 2024)
EndedAt: 2024-12-24 00:59:09 -0500 (Tue, 24 Dec 2024)
EllapsedTime: 191.3 seconds
RetCode: 0
Status:   OK  
CheckDir: PhyloProfile.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:PhyloProfile.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings PhyloProfile_1.99.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/PhyloProfile.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘PhyloProfile/DESCRIPTION’ ... OK
* this is package ‘PhyloProfile’ version ‘1.99.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 31 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 code 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 loading without being on the library search path ... 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

PhyloProfile.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL PhyloProfile
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-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) (2024-10-21 r87258) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 22 ]
> 
> proc.time()
   user  system elapsed 
  7.677   0.490   8.161 

Example timings

PhyloProfile.Rcheck/PhyloProfile-Ex.timings

nameusersystemelapsed
addDimRedTaxaColors1.1480.1021.251
addFeatureColors0.0240.0070.031
addRankDivisionPlot0.6680.0390.707
calcPresSpec0.0320.0010.033
checkColorPalette0.0010.0000.001
checkInputValidity0.0040.0000.004
checkNewick0.0020.0000.002
checkOmaID000
checkOverlapDomains0.0130.0010.015
clusterDataDend0.0170.0000.017
compareMedianTaxonGroups0.0210.0010.023
compareTaxonGroups0.0300.0000.031
createArchiPlot2.0140.0182.033
createDimRedPlotData0.5890.0340.623
createGeneAgePlot0.1940.0020.195
createLongMatrix0.0120.0060.018
createPercentageDistributionData0.0640.0070.071
createProfileFromOma0.0000.0010.000
createUnrootedTree0.0110.0000.011
createVarDistPlot0.1570.0030.160
createVariableDistributionData0.0050.0040.010
createVariableDistributionDataSubset0.0070.0000.008
dataCustomizedPlot0.0290.0010.030
dataFeatureTaxGroup0.0110.0010.012
dataMainPlot0.0330.0080.042
dataVarDistTaxGroup0.0040.0020.006
dimReduction1.0950.0461.141
estimateGeneAge0.1150.0030.119
fastaParser0.0270.0010.029
featureDistTaxPlot0.1710.0010.171
filterProfileData0.1150.0240.139
fromInputToProfile0.1020.0070.110
geneAgePlotDf0.0070.0000.007
generateSinglePlot0.3260.0010.327
getAllDomainsOma000
getAllFastaOma000
getCommonAncestor0.0420.0030.045
getCoreGene0.0820.0010.083
getDataClustering0.0140.0030.017
getDataForOneOma000
getDendrogram0.0420.0020.044
getDistanceMatrix0.0150.0000.015
getDomainFolder0.0000.0000.001
getFastaFromFasInput0.0130.0000.013
getFastaFromFile0.0090.0000.009
getFastaFromFolder0.0060.0000.006
getIDsRank0.0150.0020.018
getInputTaxaID0.0030.0000.002
getInputTaxaName0.0100.0000.009
getNameList0.0080.0270.036
getOmaDataForOneOrtholog0.0000.0000.001
getOmaDomainFromURL0.0000.0010.000
getOmaMembers000
getQualColForVector0.0000.0000.001
getSelectedFastaOma0.0000.0000.001
getSelectedTaxonNames0.0140.0010.016
getTaxHierarchy0.0130.0010.014
getTaxonomyInfo0.0110.0010.012
getTaxonomyMatrix0.0740.0870.161
getTaxonomyRanks0.0000.0000.001
gridArrangeSharedLegend0.0000.0000.001
groupLabelDimRedData0.0460.0030.049
heatmapPlotting0.290.000.29
heatmapPlottingFast3.7190.3813.750
highlightProfilePlot0.2780.0060.285
id2name0.0040.0000.004
joinPlotMergeLegends0.5320.0000.533
linearizeArchitecture0.0070.0010.007
mainTaxonomyRank0.0000.0000.001
modifyFeatureName0.0140.0140.029
pairDomainPlotting0.3890.0020.390
parseDomainInput0.0120.0160.027
parseInfoProfile0.1260.0020.127
plotDimRed0.8250.0010.826
plotDimRed3D0.8190.0130.832
prepareDimRedData0.0440.0040.048
processNcbiTaxonomy000
processOrthoID0.1240.0360.177
qualitativeColours000
rankIndexing0.0390.0010.041
reduceProfile0.0120.0050.018
resolveOverlapFeatures0.0160.0020.016
runPhyloProfile0.0010.0000.000
singleDomainPlotting0.1770.0020.179
sortDomains0.0070.0000.007
sortDomainsByList0.0080.0000.009
sortInputTaxa0.0240.0030.027
sortTaxaFromTree0.0110.0000.011
taxonomyTableCreator0.0900.0040.094
varDistTaxPlot0.7290.0020.731
wideToLong0.0070.0090.016
xmlParser0.0150.0020.016