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This page was generated on 2024-06-11 14:44 -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 kjohnson3

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: 2024-06-11 01:21:26 -0400 (Tue, 11 Jun 2024)
EndedAt: 2024-06-11 01:25:31 -0400 (Tue, 11 Jun 2024)
EllapsedTime: 245.9 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: aarch64-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 Ventura 13.6.5
* 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-arm64/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: aarch64-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 
  7.121   0.536  10.197 

Example timings

PhyloProfile.Rcheck/PhyloProfile-Ex.timings

nameusersystemelapsed
addRankDivisionPlot1.6380.0652.508
calcPresSpec0.0250.0060.044
checkInputValidity0.0080.0020.012
checkNewick0.0030.0010.006
checkOmaID0.0000.0010.001
clusterDataDend0.0170.0030.034
compareMedianTaxonGroups0.0220.0040.028
compareTaxonGroups0.0280.0050.034
createArchiPlot0.4890.0200.672
createGeneAgePlot0.2150.0040.374
createLongMatrix0.0220.0060.049
createPercentageDistributionData0.0590.0160.135
createProfileFromOma0.0000.0000.001
createUnrootedTree0.0120.0020.022
createVarDistPlot0.1310.0050.237
createVariableDistributionData0.0080.0030.017
createVariableDistributionDataSubset0.0070.0020.016
dataCustomizedPlot0.0470.0030.091
dataFeatureTaxGroup0.0150.0020.028
dataMainPlot0.0220.0060.045
dataVarDistTaxGroup0.0060.0020.010
estimateGeneAge0.0890.0130.180
fastaParser0.0430.0030.081
featureDistTaxPlot0.2180.0070.408
filterProfileData0.0680.0230.149
fromInputToProfile0.0730.0160.135
geneAgePlotDf0.0040.0010.008
generateSinglePlot0.5490.0150.854
getAllDomainsOma0.0010.0000.000
getAllFastaOma000
getCommonAncestor0.0310.0040.053
getCoreGene0.0480.0120.089
getDataClustering0.0120.0020.022
getDataForOneOma000
getDendrogram0.0420.0040.069
getDistanceMatrix0.0130.0020.023
getDomainFolder000
getFastaFromFasInput0.0160.0020.027
getFastaFromFile0.0100.0020.016
getFastaFromFolder0.0080.0020.015
getIDsRank0.0250.0040.044
getInputTaxaID0.0030.0010.005
getInputTaxaName0.0100.0040.024
getNameList0.0170.0170.048
getOmaDataForOneOrtholog0.0010.0000.000
getOmaDomainFromURL000
getOmaMembers000
getQualColForVector0.0000.0000.001
getSelectedFastaOma0.0000.0000.001
getSelectedTaxonNames0.0160.0050.030
getTaxHierarchy0.0160.0020.027
getTaxonomyInfo0.0430.0020.067
getTaxonomyMatrix0.0800.0570.200
getTaxonomyRanks0.0010.0000.000
gridArrangeSharedLegend0.7770.0121.219
heatmapPlotting0.2550.0050.447
highlightProfilePlot0.2950.0070.369
id2name0.0050.0010.005
mainTaxonomyRank0.0000.0000.001
modifyFeatureName0.0000.0000.001
pairDomainPlotting000
parseDomainInput0.0150.0090.024
parseInfoProfile0.0410.0160.057
processNcbiTaxonomy0.0700.0460.207
processOrthoID0.0830.0500.268
qualitativeColours0.0000.0010.000
rankIndexing000
reduceProfile0.0150.0050.035
runPhyloProfile0.0800.0460.261
singleDomainPlotting0.0000.0000.001
sortDomains000
sortInputTaxa0.0310.0090.053
sortTaxaFromTree0.0110.0020.012
taxonomyTableCreator0.1120.0080.204
varDistTaxPlot0.8050.0150.946
wideToLong0.0140.0060.025
xmlParser0.0170.0030.025