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This page was generated on 2024-06-21 17:41 -0400 (Fri, 21 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4758
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4492
merida1macOS 12.7.4 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4506
kjohnson1macOS 13.6.6 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4464
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: 2024-06-19 14:00 -0400 (Wed, 19 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
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for PhyloProfile on merida1

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: 2024-06-20 09:12:01 -0400 (Thu, 20 Jun 2024)
EndedAt: 2024-06-20 09:18:22 -0400 (Thu, 20 Jun 2024)
EllapsedTime: 381.5 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 12.7.4
* 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 
 14.162   1.051  19.087 

Example timings

PhyloProfile.Rcheck/PhyloProfile-Ex.timings

nameusersystemelapsed
addRankDivisionPlot2.3640.1782.997
calcPresSpec0.0500.0120.072
checkInputValidity0.0180.0040.029
checkNewick0.0050.0020.009
checkOmaID0.0000.0000.001
clusterDataDend0.0400.0080.059
compareMedianTaxonGroups0.0620.0120.090
compareTaxonGroups0.0850.0170.130
createArchiPlot1.2890.0671.639
createGeneAgePlot0.5300.0070.655
createLongMatrix0.0490.0220.090
createPercentageDistributionData0.1350.0260.194
createProfileFromOma0.0000.0000.001
createUnrootedTree0.0350.0020.042
createVarDistPlot0.3120.0070.380
createVariableDistributionData0.0150.0110.030
createVariableDistributionDataSubset0.0140.0040.020
dataCustomizedPlot0.0590.0060.078
dataFeatureTaxGroup0.0300.0040.037
dataMainPlot0.0510.0240.092
dataVarDistTaxGroup0.0100.0030.016
estimateGeneAge0.2180.0200.285
fastaParser0.0840.0040.101
featureDistTaxPlot0.5010.0100.632
filterProfileData0.1620.0710.267
fromInputToProfile0.1770.0330.253
geneAgePlotDf0.0080.0000.011
generateSinglePlot1.1890.0241.447
getAllDomainsOma0.0000.0000.001
getAllFastaOma0.0000.0000.001
getCommonAncestor0.0920.0120.128
getCoreGene0.1120.0160.155
getDataClustering0.0310.0050.044
getDataForOneOma0.0000.0000.001
getDendrogram0.1060.0050.131
getDistanceMatrix0.0290.0030.041
getDomainFolder0.0010.0000.001
getFastaFromFasInput0.0330.0020.040
getFastaFromFile0.0230.0020.029
getFastaFromFolder0.0170.0020.020
getIDsRank0.0590.0060.078
getInputTaxaID0.0040.0020.011
getInputTaxaName0.0240.0060.037
getNameList0.0460.0660.152
getOmaDataForOneOrtholog0.0000.0010.000
getOmaDomainFromURL0.0000.0010.001
getOmaMembers0.0000.0010.001
getQualColForVector0.0010.0000.001
getSelectedFastaOma000
getSelectedTaxonNames0.0360.0090.061
getTaxHierarchy0.0350.0040.052
getTaxonomyInfo0.0520.0050.072
getTaxonomyMatrix0.2410.2530.625
getTaxonomyRanks0.0010.0010.001
gridArrangeSharedLegend1.7240.0242.162
heatmapPlotting0.6460.0100.775
highlightProfilePlot0.7180.0110.897
id2name0.0080.0020.012
mainTaxonomyRank0.0010.0010.002
modifyFeatureName000
pairDomainPlotting0.0000.0010.001
parseDomainInput0.0380.0410.106
parseInfoProfile0.1180.0560.233
processNcbiTaxonomy0.1700.1230.469
processOrthoID0.1520.0580.243
qualitativeColours0.0000.0000.001
rankIndexing0.0000.0010.001
reduceProfile0.0280.0180.055
runPhyloProfile0.1540.0590.248
singleDomainPlotting0.0000.0010.001
sortDomains0.0010.0010.002
sortInputTaxa0.0700.0120.102
sortTaxaFromTree0.0330.0020.038
taxonomyTableCreator0.2730.0140.362
varDistTaxPlot2.1040.0292.689
wideToLong0.0300.0190.062
xmlParser0.0330.0070.048