Vinh Tran
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/PhyloProfile |
| Branch: RELEASE_3_10 |
| Last Commit: b2c5af6 |
| Last Changed Date: 2020-03-14 14:47:07 -0400 (Sat, 14 Mar 2020) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:32:54 -0400 (Wed, 15 Apr 2020).
| Package 1261/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| PhyloProfile 1.0.7 Vinh Tran
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: PhyloProfile |
| Version: 1.0.7 |
| Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PhyloProfile.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings PhyloProfile_1.0.7.tar.gz |
| StartedAt: 2020-04-15 05:30:40 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 05:33:57 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 197.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: PhyloProfile.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PhyloProfile.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings PhyloProfile_1.0.7.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/PhyloProfile.Rcheck' * using R version 3.6.3 (2020-02-29) * 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 '1.0.7' * 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
PhyloProfile.Rcheck/00install.out
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### Running command:
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### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/PhyloProfile_1.0.7.tar.gz && rm -rf PhyloProfile.buildbin-libdir && mkdir PhyloProfile.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=PhyloProfile.buildbin-libdir PhyloProfile_1.0.7.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL PhyloProfile_1.0.7.zip && rm PhyloProfile_1.0.7.tar.gz PhyloProfile_1.0.7.zip
###
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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
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
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_1.0.7.zip
* DONE (PhyloProfile)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'PhyloProfile' successfully unpacked and MD5 sums checked
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PhyloProfile.Rcheck/tests_i386/testthat.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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")
== testthat results ===========================================================
[ OK: 20 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
6.79 0.59 7.34
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PhyloProfile.Rcheck/tests_x64/testthat.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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")
== testthat results ===========================================================
[ OK: 20 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
7.35 0.51 7.86
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PhyloProfile.Rcheck/examples_i386/PhyloProfile-Ex.timings
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PhyloProfile.Rcheck/examples_x64/PhyloProfile-Ex.timings
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