Back to Multiple platform build/check report for BioC 3.13
ABCDEFGHIJKLMNO[P]QRSTUVWXYZ

This page was generated on 2021-10-15 15:06:16 -0400 (Fri, 15 Oct 2021).

CHECK results for PhyloProfile on tokay2

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: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PhyloProfile.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings PhyloProfile_1.6.6.tar.gz
StartedAt: 2021-10-15 03:25:20 -0400 (Fri, 15 Oct 2021)
EndedAt: 2021-10-15 03:28:52 -0400 (Fri, 15 Oct 2021)
EllapsedTime: 212.1 seconds
RetCode: 0
Status:   OK  
CheckDir: PhyloProfile.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PhyloProfile.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings PhyloProfile_1.6.6.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/PhyloProfile.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/PhyloProfile_1.6.6.tar.gz && rm -rf PhyloProfile.buildbin-libdir && mkdir PhyloProfile.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=PhyloProfile.buildbin-libdir PhyloProfile_1.6.6.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL PhyloProfile_1.6.6.zip && rm PhyloProfile_1.6.6.tar.gz PhyloProfile_1.6.6.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  9  500k    9 47277    0     0   301k      0  0:00:01 --:--:--  0:00:01  301k
100  500k  100  500k    0     0  1477k      0 --:--:-- --:--:-- --:--:-- 1476k

install for i386

* installing *source* package 'PhyloProfile' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'PhyloProfile'
    finding HTML links ... done
    calcPresSpec                            html  
    checkInputValidity                      html  
    checkNewick                             html  
    checkOmaID                              html  
    clusterDataDend                         html  
    compareMedianTaxonGroups                html  
    compareTaxonGroups                      html  
    createArchiPlot                         html  
    createGeneAgePlot                       html  
    createLongMatrix                        html  
    createPercentageDistributionData        html  
    createProfileFromOma                    html  
    createRootedTree                        html  
    createVarDistPlot                       html  
    createVariableDistributionData          html  
    createVariableDistributionDataSubset    html  
    dataCustomizedPlot                      html  
    dataFeatureTaxGroup                     html  
    dataMainPlot                            html  
    dataVarDistTaxGroup                     html  
    distributionTest                        html  
    estimateGeneAge                         html  
    fastaParser                             html  
    featureDistTaxPlot                      html  
    filterProfileData                       html  
    filteredProfile                         html  
    finalProcessedProfile                   html  
    fromInputToProfile                      html  
    fullProcessedProfile                    html  
    geneAgePlotDf                           html  
    generateSinglePlot                      html  
    getAllDomainsOma                        html  
    getAllFastaOma                          html  
    getCommonAncestor                       html  
    getCoreGene                             html  
    getDataClustering                       html  
    getDataForOneOma                        html  
    getDendrogram                           html  
    getDistanceMatrix                       html  
    getDomainFolder                         html  
    getFastaFromFasInput                    html  
    getFastaFromFile                        html  
    getFastaFromFolder                      html  
    getIDsRank                              html  
    getInputTaxaID                          html  
    getInputTaxaName                        html  
    getNameList                             html  
    getOmaDataForOneOrtholog                html  
    getOmaDomainFromURL                     html  
    getOmaMembers                           html  
    getQualColForVector                     html  
    getSelectedFastaOma                     html  
    getSelectedTaxonNames                   html  
    getTaxonomyInfo                         html  
    getTaxonomyMatrix                       html  
    getTaxonomyRanks                        html  
    gridArrangeSharedLegend                 html  
    heatmapPlotting                         html  
    highlightProfilePlot                    html  
    idList                                  html  
    mainLongRaw                             html  
    mainTaxonomyRank                        html  
    pairDomainPlotting                      html  
    parseDomainInput                        html  
    parseInfoProfile                        html  
    ppTaxonomyMatrix                        html  
    ppTree                                  html  
    processNcbiTaxonomy                     html  
    profileWithTaxonomy                     html  
    qualitativeColours                      html  
    rankIndexing                            html  
    rankList                                html  
    reduceProfile                           html  
    runPhyloProfile                         html  
    singleDomainPlotting                    html  
    sortDomains                             html  
    sortInputTaxa                           html  
    sortTaxaFromTree                        html  
    superTaxonProfile                       html  
    taxa2dist                               html  
    taxonNamesReduced                       html  
    taxonomyMatrix                          html  
    taxonomyTableCreator                    html  
    varDistTaxPlot                          html  
    wideToLong                              html  
    xmlParser                               html  
** 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

install for x64

* installing *source* package 'PhyloProfile' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'PhyloProfile' as PhyloProfile_1.6.6.zip
* DONE (PhyloProfile)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'PhyloProfile' successfully unpacked and MD5 sums checked

Tests output

PhyloProfile.Rcheck/tests_i386/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 
   6.57    0.64    7.18 

PhyloProfile.Rcheck/tests_x64/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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 
   6.90    0.40    7.29 

Example timings

PhyloProfile.Rcheck/examples_i386/PhyloProfile-Ex.timings

nameusersystemelapsed
calcPresSpec0.050.000.04
checkInputValidity0.020.000.04
checkNewick000
checkOmaID000
clusterDataDend0.020.020.03
compareMedianTaxonGroups0.030.010.05
compareTaxonGroups0.020.030.05
createArchiPlot0.450.030.50
createGeneAgePlot0.120.000.12
createLongMatrix0.030.000.03
createPercentageDistributionData0.110.020.12
createProfileFromOma000
createRootedTree0.020.000.02
createVarDistPlot0.120.000.12
createVariableDistributionData0.020.000.02
createVariableDistributionDataSubset000
dataCustomizedPlot0.010.000.02
dataFeatureTaxGroup0.000.010.01
dataMainPlot0.020.000.02
dataVarDistTaxGroup0.010.000.01
estimateGeneAge0.100.040.13
fastaParser0.030.000.03
featureDistTaxPlot0.160.000.16
filterProfileData0.110.000.11
fromInputToProfile0.170.030.22
geneAgePlotDf0.020.000.01
generateSinglePlot0.400.000.41
getAllDomainsOma000
getAllFastaOma000
getCommonAncestor0.050.000.05
getCoreGene0.110.010.12
getDataClustering0.010.000.02
getDataForOneOma000
getDendrogram0.050.000.04
getDistanceMatrix0.020.000.02
getDomainFolder000
getFastaFromFasInput0.010.000.01
getFastaFromFile0.020.000.02
getFastaFromFolder000
getIDsRank0.030.000.03
getInputTaxaID000
getInputTaxaName0.030.000.03
getNameList0.020.000.02
getOmaDataForOneOrtholog000
getOmaDomainFromURL000
getOmaMembers000
getQualColForVector000
getSelectedFastaOma000
getSelectedTaxonNames0.000.010.02
getTaxonomyInfo0.020.020.03
getTaxonomyMatrix0.140.050.19
getTaxonomyRanks000
gridArrangeSharedLegend0.530.000.53
heatmapPlotting0.190.000.18
highlightProfilePlot0.220.000.22
mainTaxonomyRank000
pairDomainPlotting000
parseDomainInput0.010.000.02
parseInfoProfile0.100.010.11
processNcbiTaxonomy0.150.020.50
qualitativeColours000
rankIndexing000
reduceProfile0.020.000.01
runPhyloProfile0.120.040.18
singleDomainPlotting000
sortDomains000
sortInputTaxa0.100.020.10
sortTaxaFromTree0.010.000.02
taxonomyTableCreator0.140.000.14
varDistTaxPlot0.640.000.64
wideToLong0.030.000.03
xmlParser0.040.000.08

PhyloProfile.Rcheck/examples_x64/PhyloProfile-Ex.timings

nameusersystemelapsed
calcPresSpec0.030.000.03
checkInputValidity0.000.020.02
checkNewick000
checkOmaID000
clusterDataDend0.030.000.03
compareMedianTaxonGroups0.020.020.03
compareTaxonGroups0.030.000.03
createArchiPlot0.450.000.46
createGeneAgePlot0.140.010.15
createLongMatrix0.030.000.04
createPercentageDistributionData0.110.020.12
createProfileFromOma000
createRootedTree0.020.000.02
createVarDistPlot0.150.000.15
createVariableDistributionData0.020.000.02
createVariableDistributionDataSubset0.010.000.01
dataCustomizedPlot0.020.000.02
dataFeatureTaxGroup0.010.000.01
dataMainPlot0.020.000.02
dataVarDistTaxGroup000
estimateGeneAge0.130.010.14
fastaParser0.030.000.03
featureDistTaxPlot0.170.000.17
filterProfileData0.120.000.13
fromInputToProfile0.110.000.11
geneAgePlotDf0.020.000.01
generateSinglePlot0.280.020.30
getAllDomainsOma000
getAllFastaOma000
getCommonAncestor0.050.000.05
getCoreGene0.070.010.09
getDataClustering0.020.000.02
getDataForOneOma000
getDendrogram0.050.000.04
getDistanceMatrix0.010.000.02
getDomainFolder000
getFastaFromFasInput0.020.000.02
getFastaFromFile000
getFastaFromFolder0.010.000.01
getIDsRank0.020.020.03
getInputTaxaID000
getInputTaxaName0.020.000.02
getNameList0.030.000.03
getOmaDataForOneOrtholog000
getOmaDomainFromURL000
getOmaMembers000
getQualColForVector000
getSelectedFastaOma000
getSelectedTaxonNames0.000.010.01
getTaxonomyInfo0.010.000.02
getTaxonomyMatrix0.080.040.11
getTaxonomyRanks000
gridArrangeSharedLegend0.50.00.5
heatmapPlotting0.20.00.2
highlightProfilePlot0.220.000.22
mainTaxonomyRank000
pairDomainPlotting000
parseDomainInput0.000.010.02
parseInfoProfile0.080.020.09
processNcbiTaxonomy0.090.030.13
qualitativeColours000
rankIndexing000
reduceProfile0.020.000.01
runPhyloProfile0.050.050.10
singleDomainPlotting000
sortDomains0.010.000.01
sortInputTaxa0.060.010.08
sortTaxaFromTree000
taxonomyTableCreator0.130.000.12
varDistTaxPlot0.80.00.8
wideToLong0.010.000.02
xmlParser0.030.000.03