Vinh Tran
| Snapshot Date: 2024-05-29 14:00:10 -0400 (Wed, 29 May 2024) |
| git_url: https://git.bioconductor.org/packages/PhyloProfile |
| git_branch: RELEASE_3_19 |
| git_last_commit: 7bb4956 |
| git_last_commit_date: 2024-04-30 11:16:16 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-05-30 11:35:48 -0400 (Thu, 30 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4753 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4518 |
| 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 1562/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| PhyloProfile 1.18.0 (landing page) Vinh Tran
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
|
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. |
| Package: PhyloProfile |
| Version: 1.18.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PhyloProfile.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PhyloProfile_1.18.0.tar.gz |
| StartedAt: 2024-05-29 22:51:07 -0400 (Wed, 29 May 2024) |
| EndedAt: 2024-05-29 22:54:15 -0400 (Wed, 29 May 2024) |
| EllapsedTime: 187.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: PhyloProfile.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PhyloProfile.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PhyloProfile_1.18.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/PhyloProfile.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PhyloProfile/DESCRIPTION’ ... OK
* this is package ‘PhyloProfile’ version ‘1.18.0’
* 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 ... NOTE
License stub is invalid DCF.
* 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 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 ... NOTE
checkRd: (-1) addRankDivisionPlot.Rd:75: Lost braces; missing escapes or markup?
75 | Vinh Tran {tran@bio.uni-frankfurt.de}
| ^
checkRd: (-1) calcPresSpec.Rd:33: Lost braces; missing escapes or markup?
33 | Vinh Tran {tran@bio.uni-frankfurt.de}
| ^
checkRd: (-1) checkInputValidity.Rd:29: Lost braces; missing escapes or markup?
29 | Vinh Tran {tran@bio.uni-frankfurt.de}
| ^
checkRd: (-1) checkNewick.Rd:32: Lost braces; missing escapes or markup?
32 | Vinh Tran {tran@bio.uni-frankfurt.de}
| ^
checkRd: (-1) checkOmaID.Rd:23: Lost braces; missing escapes or markup?
23 | Vinh Tran {tran@bio.uni-frankfurt.de}
| ^
checkRd: (-1) clusterDataDend.Rd:39: Lost braces; missing escapes or markup?
39 | Vinh Tran {tran@bio.uni-frankfurt.de}
| ^
checkRd: (-1) createArchiPlot.Rd:60: Lost braces; missing escapes or markup?
60 | Vinh Tran {tran@bio.uni-frankfurt.de}
| ^
checkRd: (-1) createGeneAgePlot.Rd:33: Lost braces; missing escapes or markup?
33 | Vinh Tran {tran@bio.uni-frankfurt.de}
| ^
checkRd: (-1) createLongMatrix.Rd:32: Lost braces; missing escapes or markup?
32 | Vinh Tran {tran@bio.uni-frankfurt.de}
| ^
checkRd: (-1) createPercentageDistributionData.Rd:35: Lost braces; missing escapes or markup?
35 | Vinh Tran {tran@bio.uni-frankfurt.de}
| ^
checkRd: (-1) createProfileFromOma.Rd:29: Lost braces; missing escapes or markup?
29 | Vinh Tran {tran@bio.uni-frankfurt.de}
| ^
checkRd: (-1) createUnrootedTree.Rd:28: Lost braces; missing escapes or markup?
28 | Vinh Tran {tran@bio.uni-frankfurt.de}
| ^
checkRd: (-1) createVarDistPlot.Rd:56: Lost braces; missing escapes or markup?
56 | Vinh Tran {tran@bio.uni-frankfurt.de}
| ^
checkRd: (-1) createVariableDistributionData.Rd:36: Lost braces; missing escapes or markup?
36 | Vinh Tran {tran@bio.uni-frankfurt.de}
| ^
checkRd: (-1) createVariableDistributionDataSubset.Rd:50: Lost braces; missing escapes or markup?
50 | Vinh Tran {tran@bio.uni-frankfurt.de}
| ^
checkRd: (-1) dataCustomizedPlot.Rd:42: Lost braces; missing escapes or markup?
42 | Vinh Tran {tran@bio.uni-frankfurt.de}
| ^
checkRd: (-1) dataMainPlot.Rd:34: Lost braces; missing escapes or markup?
34 | Vinh Tran {tran@bio.uni-frankfurt.de}
| ^
checkRd: (-1) estimateGeneAge.Rd:64: Lost braces; missing escapes or markup?
64 | Vinh Tran {tran@bio.uni-frankfurt.de}
| ^
checkRd: (-1) fastaParser.Rd:29: Lost braces; missing escapes or markup?
29 | Vinh Tran {tran@bio.uni-frankfurt.de}
| ^
checkRd: (-1) featureDistTaxPlot.Rd:51: Lost braces; missing escapes or markup?
51 | Vinh Tran {tran@bio.uni-frankfurt.de}
| ^
checkRd: (-1) filterProfileData.Rd:110: Lost braces; missing escapes or markup?
110 | Vinh Tran {tran@bio.uni-frankfurt.de}
| ^
checkRd: (-1) filteredProfile.Rd:13: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) filteredProfile.Rd:14-15: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) filteredProfile.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) filteredProfile.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) filteredProfile.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) filteredProfile.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) filteredProfile.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) filteredProfile.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) filteredProfile.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) filteredProfile.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) filteredProfile.Rd:24-25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) filteredProfile.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) filteredProfile.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) filteredProfile.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) filteredProfile.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) filteredProfile.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) filteredProfile.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) filteredProfile.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) filteredProfile.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) filteredProfile.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) finalProcessedProfile.Rd:13: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) finalProcessedProfile.Rd:14-15: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) finalProcessedProfile.Rd:16-17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) finalProcessedProfile.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) finalProcessedProfile.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) finalProcessedProfile.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) finalProcessedProfile.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) finalProcessedProfile.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) finalProcessedProfile.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) finalProcessedProfile.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) finalProcessedProfile.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fromInputToProfile.Rd:112: Lost braces; missing escapes or markup?
112 | Vinh Tran {tran@bio.uni-frankfurt.de}
| ^
checkRd: (-1) fullProcessedProfile.Rd:13-14: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fullProcessedProfile.Rd:15: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fullProcessedProfile.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fullProcessedProfile.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fullProcessedProfile.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fullProcessedProfile.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fullProcessedProfile.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fullProcessedProfile.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fullProcessedProfile.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fullProcessedProfile.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fullProcessedProfile.Rd:24-25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fullProcessedProfile.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fullProcessedProfile.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fullProcessedProfile.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) geneAgePlotDf.Rd:32: Lost braces; missing escapes or markup?
32 | Vinh Tran {tran@bio.uni-frankfurt.de}
| ^
checkRd: (-1) generateSinglePlot.Rd:47: Lost braces; missing escapes or markup?
47 | Vinh Tran {tran@bio.uni-frankfurt.de}
| ^
checkRd: (-1) getAllDomainsOma.Rd:29: Lost braces; missing escapes or markup?
29 | Vinh Tran {tran@bio.uni-frankfurt.de}
| ^
checkRd: (-1) getAllFastaOma.Rd:27: Lost braces; missing escapes or markup?
27 | Vinh Tran {tran@bio.uni-frankfurt.de}
| ^
checkRd: (-1) getCoreGene.Rd:72: Lost braces; missing escapes or markup?
72 | Vinh Tran {tran@bio.uni-frankfurt.de}
| ^
checkRd: (-1) getDataForOneOma.Rd:28: Lost braces; missing escapes or markup?
28 | Vinh Tran {tran@bio.uni-frankfurt.de}
| ^
checkRd: (-1) getDendrogram.Rd:34: Lost braces; missing escapes or markup?
34 | Vinh Tran {tran@bio.uni-frankfurt.de}
| ^
checkRd: (-1) getDomainFolder.Rd:29: Lost braces; missing escapes or markup?
29 | Vinh Tran {tran@bio.uni-frankfurt.de}
| ^
checkRd: (-1) getFastaFromFasInput.Rd:29: Lost braces; missing escapes or markup?
29 | Vinh Tran {tran@bio.uni-frankfurt.de}
| ^
checkRd: (-1) getFastaFromFile.Rd:29: Lost braces; missing escapes or markup?
29 | Vinh Tran {tran@bio.uni-frankfurt.de}
| ^
checkRd: (-1) getFastaFromFolder.Rd:43: Lost braces; missing escapes or markup?
43 | Vinh Tran {tran@bio.uni-frankfurt.de}
| ^
checkRd: (-1) getIDsRank.Rd:38: Lost braces; missing escapes or markup?
38 | Vinh Tran {tran@bio.uni-frankfurt.de}
| ^
checkRd: (-1) getInputTaxaID.Rd:26: Lost braces; missing escapes or markup?
26 | Vinh Tran {tran@bio.uni-frankfurt.de}
| ^
checkRd: (-1) getInputTaxaName.Rd:33: Lost braces; missing escapes or markup?
33 | Vinh Tran {tran@bio.uni-frankfurt.de}
| ^
checkRd: (-1) getNameList.Rd:24: Lost braces; missing escapes or markup?
24 | Vinh Tran {tran@bio.uni-frankfurt.de}
| ^
checkRd: (-1) getOmaDataForOneOrtholog.Rd:24: Lost braces; missing escapes or markup?
24 | Vinh Tran {tran@bio.uni-frankfurt.de}
| ^
checkRd: (-1) getOmaDomainFromURL.Rd:25: Lost braces; missing escapes or markup?
25 | Vinh Tran {tran@bio.uni-frankfurt.de}
| ^
checkRd: (-1) getOmaMembers.Rd:28: Lost braces; missing escapes or markup?
28 | Carla Mölbert {carla.moelbert@gmx.de}
| ^
checkRd: (-1) getQualColForVector.Rd:27: Lost braces; missing escapes or markup?
27 | Vinh Tran {tran@bio.uni-frankfurt.de}
| ^
checkRd: (-1) getSelectedFastaOma.Rd:29: Lost braces; missing escapes or markup?
29 | Vinh Tran {tran@bio.uni-frankfurt.de}
| ^
checkRd: (-1) getSelectedTaxonNames.Rd:45: Lost braces; missing escapes or markup?
45 | Vinh Tran {tran@bio.uni-frankfurt.de}
| ^
checkRd: (-1) getTaxHierarchy.Rd:32: Lost braces; missing escapes or markup?
32 | Vinh Tran {tran@bio.uni-frankfurt.de}
| ^
checkRd: (-1) getTaxonomyInfo.Rd:32: Lost braces; missing escapes or markup?
32 | Vinh Tran {tran@bio.uni-frankfurt.de}
| ^
checkRd: (-1) getTaxonomyMatrix.Rd:33: Lost braces; missing escapes or markup?
33 | Vinh Tran {tran@bio.uni-frankfurt.de}
| ^
checkRd: (-1) heatmapPlotting.Rd:69: Lost braces; missing escapes or markup?
69 | Vinh Tran {tran@bio.uni-frankfurt.de}
| ^
checkRd: (-1) highlightProfilePlot.Rd:73: Lost braces; missing escapes or markup?
73 | Vinh Tran {tran@bio.uni-frankfurt.de}
| ^
checkRd: (-1) id2name.Rd:31: Lost braces; missing escapes or markup?
31 | Vinh Tran {tran@bio.uni-frankfurt.de}
| ^
checkRd: (-1) mainLongRaw.Rd:13: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mainLongRaw.Rd:14: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mainLongRaw.Rd:15: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mainLongRaw.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mainLongRaw.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mainTaxonomyRank.Rd:19: Lost braces; missing escapes or markup?
19 | Vinh Tran {tran@bio.uni-frankfurt.de}
| ^
checkRd: (-1) modifyFeatureName.Rd:32: Lost braces; missing escapes or markup?
32 | Vinh Tran {tran@bio.uni-frankfurt.de}
| ^
checkRd: (-1) pairDomainPlotting.Rd:59: Lost braces; missing escapes or markup?
59 | Vinh Tran {tran@bio.uni-frankfurt.de}
| ^
checkRd: (-1) parseDomainInput.Rd:40: Lost braces; missing escapes or markup?
40 | Vinh Tran {tran@bio.uni-frankfurt.de}
| ^
checkRd: (-1) parseInfoProfile.Rd:48: Lost braces; missing escapes or markup?
48 | Vinh Tran {tran@bio.uni-frankfurt.de}
| ^
checkRd: (-1) ppTaxonomyMatrix.Rd:13: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ppTaxonomyMatrix.Rd:14: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ppTaxonomyMatrix.Rd:15: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ppTaxonomyMatrix.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) processNcbiTaxonomy.Rd:39: Lost braces; missing escapes or markup?
39 | Vinh Tran {tran@bio.uni-frankfurt.de}
| ^
checkRd: (-1) processOrthoID.Rd:15: Lost braces; missing escapes or markup?
15 | <taxID:orthoID>. New column {orthoFreq} specifies if the ortholog IDs are
| ^
checkRd: (-1) processOrthoID.Rd:29: Lost braces; missing escapes or markup?
29 | Vinh Tran {tran@bio.uni-frankfurt.de}
| ^
checkRd: (-1) profileWithTaxonomy.Rd:13: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) profileWithTaxonomy.Rd:14: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) profileWithTaxonomy.Rd:15: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) profileWithTaxonomy.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) profileWithTaxonomy.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) profileWithTaxonomy.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) profileWithTaxonomy.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) profileWithTaxonomy.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) profileWithTaxonomy.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) profileWithTaxonomy.Rd:22-23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) profileWithTaxonomy.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) profileWithTaxonomy.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rankIndexing.Rd:29: Lost braces; missing escapes or markup?
29 | Vinh Tran {tran@bio.uni-frankfurt.de}
| ^
checkRd: (-1) reduceProfile.Rd:33: Lost braces; missing escapes or markup?
33 | Vinh Tran {tran@bio.uni-frankfurt.de}
| ^
checkRd: (-1) singleDomainPlotting.Rd:78: Lost braces; missing escapes or markup?
78 | Vinh Tran {tran@bio.uni-frankfurt.de}
| ^
checkRd: (-1) sortDomains.Rd:41: Lost braces; missing escapes or markup?
41 | Vinh Tran {tran@bio.uni-frankfurt.de}
| ^
checkRd: (-1) sortInputTaxa.Rd:45: Lost braces; missing escapes or markup?
45 | Vinh Tran {tran@bio.uni-frankfurt.de}
| ^
checkRd: (-1) sortTaxaFromTree.Rd:30: Lost braces; missing escapes or markup?
30 | Vinh Tran {tran@bio.uni-frankfurt.de}
| ^
checkRd: (-1) taxonNamesReduced.Rd:13: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) taxonNamesReduced.Rd:14: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) taxonNamesReduced.Rd:15: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) taxonNamesReduced.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) taxonomyTableCreator.Rd:39: Lost braces; missing escapes or markup?
39 | Vinh Tran {tran@bio.uni-frankfurt.de}
| ^
checkRd: (-1) varDistTaxPlot.Rd:50: Lost braces; missing escapes or markup?
50 | Vinh Tran {tran@bio.uni-frankfurt.de}
| ^
checkRd: (-1) wideToLong.Rd:27: Lost braces; missing escapes or markup?
27 | Vinh Tran {tran@bio.uni-frankfurt.de}
| ^
checkRd: (-1) xmlParser.Rd:27: Lost braces; missing escapes or markup?
27 | Vinh Tran {tran@bio.uni-frankfurt.de}
| ^
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.19-bioc/meat/PhyloProfile.Rcheck/00check.log’
for details.
PhyloProfile.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL PhyloProfile ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/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)
PhyloProfile.Rcheck/tests/testthat.Rout
R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
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
8.224 0.659 8.966
PhyloProfile.Rcheck/PhyloProfile-Ex.timings
| name | user | system | elapsed | |
| addRankDivisionPlot | 1.434 | 0.080 | 1.528 | |
| calcPresSpec | 0.029 | 0.007 | 0.039 | |
| checkInputValidity | 0.009 | 0.002 | 0.012 | |
| checkNewick | 0.003 | 0.001 | 0.004 | |
| checkOmaID | 0.000 | 0.000 | 0.001 | |
| clusterDataDend | 0.020 | 0.004 | 0.024 | |
| compareMedianTaxonGroups | 0.030 | 0.006 | 0.037 | |
| compareTaxonGroups | 0.040 | 0.007 | 0.049 | |
| createArchiPlot | 0.655 | 0.029 | 0.692 | |
| createGeneAgePlot | 0.298 | 0.004 | 0.306 | |
| createLongMatrix | 0.027 | 0.009 | 0.036 | |
| createPercentageDistributionData | 0.072 | 0.017 | 0.090 | |
| createProfileFromOma | 0 | 0 | 0 | |
| createUnrootedTree | 0.017 | 0.001 | 0.019 | |
| createVarDistPlot | 0.168 | 0.005 | 0.176 | |
| createVariableDistributionData | 0.008 | 0.006 | 0.014 | |
| createVariableDistributionDataSubset | 0.009 | 0.003 | 0.012 | |
| dataCustomizedPlot | 0.039 | 0.003 | 0.042 | |
| dataFeatureTaxGroup | 0.019 | 0.002 | 0.022 | |
| dataMainPlot | 0.029 | 0.009 | 0.038 | |
| dataVarDistTaxGroup | 0.006 | 0.002 | 0.008 | |
| estimateGeneAge | 0.108 | 0.014 | 0.122 | |
| fastaParser | 0.047 | 0.003 | 0.050 | |
| featureDistTaxPlot | 0.265 | 0.006 | 0.274 | |
| filterProfileData | 0.081 | 0.032 | 0.114 | |
| fromInputToProfile | 0.098 | 0.018 | 0.119 | |
| geneAgePlotDf | 0.006 | 0.001 | 0.007 | |
| generateSinglePlot | 0.609 | 0.014 | 0.629 | |
| getAllDomainsOma | 0 | 0 | 0 | |
| getAllFastaOma | 0.000 | 0.000 | 0.001 | |
| getCommonAncestor | 0.040 | 0.006 | 0.049 | |
| getCoreGene | 0.050 | 0.010 | 0.061 | |
| getDataClustering | 0.015 | 0.003 | 0.017 | |
| getDataForOneOma | 0 | 0 | 0 | |
| getDendrogram | 0.059 | 0.003 | 0.063 | |
| getDistanceMatrix | 0.016 | 0.002 | 0.020 | |
| getDomainFolder | 0 | 0 | 0 | |
| getFastaFromFasInput | 0.019 | 0.001 | 0.021 | |
| getFastaFromFile | 0.013 | 0.002 | 0.015 | |
| getFastaFromFolder | 0.008 | 0.002 | 0.010 | |
| getIDsRank | 0.031 | 0.003 | 0.035 | |
| getInputTaxaID | 0.003 | 0.001 | 0.004 | |
| getInputTaxaName | 0.014 | 0.003 | 0.018 | |
| getNameList | 0.024 | 0.025 | 0.049 | |
| getOmaDataForOneOrtholog | 0.001 | 0.000 | 0.000 | |
| getOmaDomainFromURL | 0.000 | 0.000 | 0.001 | |
| getOmaMembers | 0.000 | 0.001 | 0.001 | |
| getQualColForVector | 0 | 0 | 0 | |
| getSelectedFastaOma | 0.000 | 0.001 | 0.000 | |
| getSelectedTaxonNames | 0.019 | 0.005 | 0.025 | |
| getTaxHierarchy | 0.018 | 0.002 | 0.020 | |
| getTaxonomyInfo | 0.033 | 0.003 | 0.036 | |
| getTaxonomyMatrix | 0.105 | 0.098 | 0.209 | |
| getTaxonomyRanks | 0 | 0 | 0 | |
| gridArrangeSharedLegend | 0.949 | 0.015 | 0.975 | |
| heatmapPlotting | 0.321 | 0.006 | 0.330 | |
| highlightProfilePlot | 0.381 | 0.006 | 0.392 | |
| id2name | 0.005 | 0.001 | 0.005 | |
| mainTaxonomyRank | 0.001 | 0.001 | 0.000 | |
| modifyFeatureName | 0.001 | 0.000 | 0.000 | |
| pairDomainPlotting | 0.000 | 0.001 | 0.001 | |
| parseDomainInput | 0.017 | 0.015 | 0.033 | |
| parseInfoProfile | 0.060 | 0.024 | 0.085 | |
| processNcbiTaxonomy | 0.110 | 0.081 | 0.255 | |
| processOrthoID | 0.095 | 0.055 | 0.183 | |
| qualitativeColours | 0 | 0 | 0 | |
| rankIndexing | 0.000 | 0.000 | 0.001 | |
| reduceProfile | 0.017 | 0.011 | 0.027 | |
| runPhyloProfile | 0.096 | 0.055 | 0.176 | |
| singleDomainPlotting | 0.000 | 0.001 | 0.001 | |
| sortDomains | 0 | 0 | 0 | |
| sortInputTaxa | 0.034 | 0.008 | 0.044 | |
| sortTaxaFromTree | 0.015 | 0.001 | 0.017 | |
| taxonomyTableCreator | 0.135 | 0.009 | 0.147 | |
| varDistTaxPlot | 1.092 | 0.017 | 1.120 | |
| wideToLong | 0.014 | 0.005 | 0.020 | |
| xmlParser | 0.020 | 0.003 | 0.023 | |