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This page was generated on 2024-06-11 14:42 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4757
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4491
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4522
kjohnson3macOS 13.6.5 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4468
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 1562/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PhyloProfile 1.18.0  (landing page)
Vinh Tran
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 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)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows 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 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for PhyloProfile on lconway

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: 1.18.0
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: 2024-06-09 22:13:25 -0400 (Sun, 09 Jun 2024)
EndedAt: 2024-06-09 22:16:15 -0400 (Sun, 09 Jun 2024)
EllapsedTime: 170.8 seconds
RetCode: 0
Status:   OK  
CheckDir: PhyloProfile.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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.


Installation output

PhyloProfile.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL PhyloProfile
###
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* 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)

Tests output

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 
  7.549   0.555   8.121 

Example timings

PhyloProfile.Rcheck/PhyloProfile-Ex.timings

nameusersystemelapsed
addRankDivisionPlot1.3230.0581.384
calcPresSpec0.0260.0050.031
checkInputValidity0.0080.0010.011
checkNewick0.0030.0010.004
checkOmaID0.0010.0000.000
clusterDataDend0.0180.0040.022
compareMedianTaxonGroups0.0260.0050.031
compareTaxonGroups0.0390.0050.045
createArchiPlot0.5170.0190.537
createGeneAgePlot0.2340.0020.237
createLongMatrix0.0290.0070.036
createPercentageDistributionData0.0600.0130.074
createProfileFromOma0.0000.0000.001
createUnrootedTree0.0140.0010.015
createVarDistPlot0.1640.0030.168
createVariableDistributionData0.0080.0030.012
createVariableDistributionDataSubset0.0080.0020.010
dataCustomizedPlot0.0340.0020.036
dataFeatureTaxGroup0.0170.0020.019
dataMainPlot0.0260.0090.035
dataVarDistTaxGroup0.0060.0020.008
estimateGeneAge0.1050.0120.117
fastaParser0.0440.0020.045
featureDistTaxPlot0.2500.0040.254
filterProfileData0.0700.0290.099
fromInputToProfile0.0800.0130.093
geneAgePlotDf0.0040.0000.003
generateSinglePlot0.4790.0090.489
getAllDomainsOma0.0010.0000.000
getAllFastaOma000
getCommonAncestor0.0250.0040.033
getCoreGene0.0580.0100.070
getDataClustering0.0140.0030.016
getDataForOneOma0.0000.0000.001
getDendrogram0.0550.0030.058
getDistanceMatrix0.0170.0020.019
getDomainFolder0.0000.0000.001
getFastaFromFasInput0.0190.0020.020
getFastaFromFile0.0110.0020.012
getFastaFromFolder0.0070.0020.009
getIDsRank0.0300.0030.034
getInputTaxaID0.0030.0020.004
getInputTaxaName0.0120.0030.016
getNameList0.020.020.04
getOmaDataForOneOrtholog0.0000.0000.001
getOmaDomainFromURL000
getOmaMembers0.0000.0000.001
getQualColForVector000
getSelectedFastaOma000
getSelectedTaxonNames0.0190.0040.023
getTaxHierarchy0.0160.0010.018
getTaxonomyInfo0.0260.0010.026
getTaxonomyMatrix0.0870.0810.168
getTaxonomyRanks0.0000.0000.001
gridArrangeSharedLegend0.7690.0080.778
heatmapPlotting0.2660.0030.271
highlightProfilePlot0.3400.0040.345
id2name0.0050.0010.006
mainTaxonomyRank0.0010.0000.000
modifyFeatureName000
pairDomainPlotting0.0000.0010.000
parseDomainInput0.0180.0140.032
parseInfoProfile0.0590.0230.081
processNcbiTaxonomy0.0980.0620.230
processOrthoID0.0940.0500.164
qualitativeColours000
rankIndexing000
reduceProfile0.0160.0060.023
runPhyloProfile0.0920.0450.157
singleDomainPlotting0.0000.0010.001
sortDomains0.0000.0000.001
sortInputTaxa0.0340.0060.040
sortTaxaFromTree0.0130.0010.015
taxonomyTableCreator0.1150.0060.122
varDistTaxPlot0.9420.0100.955
wideToLong0.0170.0090.026
xmlParser0.0160.0030.020