| Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-06-06 11:00:38 -0000 (Tue, 06 Jun 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4366 |
| 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 | ||||
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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. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 1494/2199 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| PhyloProfile 1.15.2 (landing page) Vinh Tran
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | |||||||||
| Package: PhyloProfile |
| Version: 1.15.2 |
| Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:PhyloProfile.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings PhyloProfile_1.15.2.tar.gz |
| StartedAt: 2023-06-06 04:08:27 -0000 (Tue, 06 Jun 2023) |
| EndedAt: 2023-06-06 04:11:33 -0000 (Tue, 06 Jun 2023) |
| EllapsedTime: 185.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: PhyloProfile.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:PhyloProfile.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings PhyloProfile_1.15.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/PhyloProfile.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘PhyloProfile/DESCRIPTION’ ... OK
* this is package ‘PhyloProfile’ version ‘1.15.2’
* 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 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 in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘PhyloProfile-vignette.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
PhyloProfile.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL PhyloProfile ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.0/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)
PhyloProfile.Rcheck/tests/testthat.Rout
R version 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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
8.105 0.346 8.452
PhyloProfile.Rcheck/PhyloProfile-Ex.timings
| name | user | system | elapsed | |
| calcPresSpec | 0.034 | 0.000 | 0.034 | |
| checkInputValidity | 0.009 | 0.000 | 0.010 | |
| checkNewick | 0.003 | 0.000 | 0.003 | |
| checkOmaID | 0 | 0 | 0 | |
| clusterDataDend | 0.033 | 0.000 | 0.033 | |
| compareMedianTaxonGroups | 0.032 | 0.004 | 0.036 | |
| compareTaxonGroups | 0.041 | 0.004 | 0.045 | |
| createArchiPlot | 1.333 | 0.111 | 1.448 | |
| createGeneAgePlot | 0.244 | 0.012 | 0.257 | |
| createLongMatrix | 0.026 | 0.001 | 0.026 | |
| createPercentageDistributionData | 0.051 | 0.023 | 0.075 | |
| createProfileFromOma | 0 | 0 | 0 | |
| createUnrootedTree | 0.017 | 0.000 | 0.018 | |
| createVarDistPlot | 0.189 | 0.031 | 0.220 | |
| createVariableDistributionData | 0.003 | 0.004 | 0.007 | |
| createVariableDistributionDataSubset | 0.005 | 0.003 | 0.008 | |
| dataCustomizedPlot | 0.018 | 0.000 | 0.018 | |
| dataFeatureTaxGroup | 0.012 | 0.004 | 0.016 | |
| dataMainPlot | 0.009 | 0.012 | 0.021 | |
| dataVarDistTaxGroup | 0.006 | 0.000 | 0.005 | |
| estimateGeneAge | 0.107 | 0.008 | 0.115 | |
| fastaParser | 0.043 | 0.008 | 0.051 | |
| featureDistTaxPlot | 0.262 | 0.016 | 0.278 | |
| filterProfileData | 0.083 | 0.000 | 0.083 | |
| fromInputToProfile | 0.089 | 0.012 | 0.103 | |
| geneAgePlotDf | 0.002 | 0.003 | 0.005 | |
| generateSinglePlot | 0.658 | 0.020 | 0.680 | |
| getAllDomainsOma | 0 | 0 | 0 | |
| getAllFastaOma | 0 | 0 | 0 | |
| getCommonAncestor | 0.043 | 0.004 | 0.047 | |
| getCoreGene | 0.060 | 0.000 | 0.059 | |
| getDataClustering | 0.013 | 0.004 | 0.016 | |
| getDataForOneOma | 0 | 0 | 0 | |
| getDendrogram | 0.052 | 0.004 | 0.056 | |
| getDistanceMatrix | 0.016 | 0.000 | 0.016 | |
| getDomainFolder | 0 | 0 | 0 | |
| getFastaFromFasInput | 0.019 | 0.000 | 0.018 | |
| getFastaFromFile | 0.012 | 0.000 | 0.013 | |
| getFastaFromFolder | 0.009 | 0.000 | 0.009 | |
| getIDsRank | 0.031 | 0.000 | 0.032 | |
| getInputTaxaID | 0.002 | 0.000 | 0.002 | |
| getInputTaxaName | 0.009 | 0.004 | 0.012 | |
| getNameList | 0.014 | 0.008 | 0.022 | |
| getOmaDataForOneOrtholog | 0.001 | 0.000 | 0.000 | |
| getOmaDomainFromURL | 0 | 0 | 0 | |
| getOmaMembers | 0.000 | 0.000 | 0.001 | |
| getQualColForVector | 0 | 0 | 0 | |
| getSelectedFastaOma | 0 | 0 | 0 | |
| getSelectedTaxonNames | 0.015 | 0.004 | 0.019 | |
| getTaxonomyInfo | 0.015 | 0.000 | 0.015 | |
| getTaxonomyMatrix | 0.076 | 0.040 | 0.116 | |
| getTaxonomyRanks | 0 | 0 | 0 | |
| gridArrangeSharedLegend | 0.794 | 0.000 | 0.796 | |
| heatmapPlotting | 0.426 | 0.000 | 0.427 | |
| highlightProfilePlot | 0.475 | 0.000 | 0.476 | |
| mainTaxonomyRank | 0.000 | 0.000 | 0.001 | |
| pairDomainPlotting | 0 | 0 | 0 | |
| parseDomainInput | 0.011 | 0.004 | 0.014 | |
| parseInfoProfile | 0.057 | 0.004 | 0.061 | |
| processNcbiTaxonomy | 0.074 | 0.032 | 0.188 | |
| processOrthoID | 0.083 | 0.010 | 0.094 | |
| qualitativeColours | 0 | 0 | 0 | |
| rankIndexing | 0.000 | 0.000 | 0.001 | |
| reduceProfile | 0.008 | 0.007 | 0.015 | |
| runPhyloProfile | 0.084 | 0.004 | 0.089 | |
| singleDomainPlotting | 0 | 0 | 0 | |
| sortDomains | 0 | 0 | 0 | |
| sortInputTaxa | 0.034 | 0.004 | 0.038 | |
| sortTaxaFromTree | 0.017 | 0.000 | 0.016 | |
| taxonomyTableCreator | 0.135 | 0.008 | 0.144 | |
| varDistTaxPlot | 1.026 | 0.016 | 1.044 | |
| wideToLong | 0.011 | 0.004 | 0.015 | |
| xmlParser | 0.023 | 0.000 | 0.025 | |