############################################################################## ############################################################################## ### ### 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 (2024-04-24) * 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 | . 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.