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This page was generated on 2024-05-04 11:36:58 -0400 (Sat, 04 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4519
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4479
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: 2024-05-03 14:00:19 -0400 (Fri, 03 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)
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
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for PhyloProfile on nebbiolo1


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: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:PhyloProfile.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings PhyloProfile_1.18.0.tar.gz
StartedAt: 2024-05-04 02:21:49 -0400 (Sat, 04 May 2024)
EndedAt: 2024-05-04 02:24:20 -0400 (Sat, 04 May 2024)
EllapsedTime: 151.3 seconds
RetCode: 0
Status:   OK  
CheckDir: PhyloProfile.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:PhyloProfile.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings PhyloProfile_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/PhyloProfile.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/PhyloProfile.Rcheck/00check.log’
for details.


Installation output

PhyloProfile.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL PhyloProfile
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘PhyloProfile’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (PhyloProfile)

Tests output

PhyloProfile.Rcheck/tests/testthat.Rout


R version 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 
  6.164   0.364   6.516 

Example timings

PhyloProfile.Rcheck/PhyloProfile-Ex.timings

nameusersystemelapsed
addRankDivisionPlot1.0210.0751.097
calcPresSpec0.0090.0150.025
checkInputValidity0.0070.0010.007
checkNewick0.0030.0000.002
checkOmaID0.0010.0000.000
clusterDataDend0.0190.0000.019
compareMedianTaxonGroups0.0200.0070.029
compareTaxonGroups0.0340.0030.039
createArchiPlot0.4890.0170.506
createGeneAgePlot0.1830.0040.187
createLongMatrix0.0150.0080.023
createPercentageDistributionData0.0630.0040.068
createProfileFromOma000
createUnrootedTree0.0070.0040.011
createVarDistPlot0.120.000.12
createVariableDistributionData0.0090.0000.009
createVariableDistributionDataSubset0.0030.0040.007
dataCustomizedPlot0.0120.0030.015
dataFeatureTaxGroup0.0120.0010.013
dataMainPlot0.0170.0070.025
dataVarDistTaxGroup0.0050.0010.005
estimateGeneAge0.0790.0000.079
fastaParser0.0330.0040.037
featureDistTaxPlot0.1740.0040.178
filterProfileData0.0640.0150.079
fromInputToProfile0.0590.0110.072
geneAgePlotDf0.0050.0030.009
generateSinglePlot0.4670.0360.504
getAllDomainsOma000
getAllFastaOma0.0000.0000.001
getCommonAncestor0.0290.0030.033
getCoreGene0.0420.0040.046
getDataClustering0.0010.0110.013
getDataForOneOma000
getDendrogram0.0420.0010.043
getDistanceMatrix0.0260.0000.026
getDomainFolder000
getFastaFromFasInput0.0140.0000.013
getFastaFromFile0.0090.0000.009
getFastaFromFolder0.0060.0000.006
getIDsRank0.0230.0000.023
getInputTaxaID0.0030.0000.003
getInputTaxaName0.0100.0000.009
getNameList0.0080.0280.036
getOmaDataForOneOrtholog0.0010.0000.000
getOmaDomainFromURL0.0000.0000.001
getOmaMembers000
getQualColForVector0.0010.0000.000
getSelectedFastaOma0.0010.0000.001
getSelectedTaxonNames0.0110.0030.016
getTaxHierarchy0.0150.0000.015
getTaxonomyInfo0.0140.0000.013
getTaxonomyMatrix0.0930.0710.164
getTaxonomyRanks0.0010.0000.001
gridArrangeSharedLegend0.6550.0040.659
heatmapPlotting0.2340.0040.238
highlightProfilePlot0.2710.0080.278
id2name0.0040.0000.004
mainTaxonomyRank0.0010.0000.000
modifyFeatureName0.0010.0000.000
pairDomainPlotting0.0000.0000.001
parseDomainInput0.0140.0110.026
parseInfoProfile0.0390.0200.060
processNcbiTaxonomy0.1050.0080.138
processOrthoID0.0810.0110.091
qualitativeColours0.0010.0000.000
rankIndexing000
reduceProfile0.0160.0000.016
runPhyloProfile0.0830.0070.090
singleDomainPlotting0.0010.0000.000
sortDomains0.0010.0000.000
sortInputTaxa0.0290.0000.028
sortTaxaFromTree0.0110.0000.011
taxonomyTableCreator0.0830.0160.100
varDistTaxPlot0.7720.0040.776
wideToLong0.0130.0040.017
xmlParser0.0130.0040.017