############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:oligoClasses.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings oligoClasses_1.69.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/oligoClasses.Rcheck’ * using R Under development (unstable) (2024-10-21 r87258) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘oligoClasses/DESCRIPTION’ ... OK * this is package ‘oligoClasses’ version ‘1.69.0’ * checking package namespace information ... OK * checking package dependencies ... INFO Packages which this enhances but not available for checking: 'doMPI', 'doRedis' * 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 ‘oligoClasses’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * 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 whether startup messages can be suppressed ... OK * checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘RSQLite’ All declared Imports should be used. Unexported object imported by a ':::' call: ‘Biobase:::assayDataEnvLock’ See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE getSequenceLengths: no visible binding for global variable ‘seqlengths’ chromosome,gSetList: no visible global function definition for ‘chromosomeList’ coerce,CNSet-CopyNumberSet: no visible global function definition for ‘totalCopynumber’ geometry,FeatureSet: no visible global function definition for ‘getPD’ Undefined global functions or variables: chromosomeList getPD seqlengths totalCopynumber * checking Rd files ... WARNING checkRd: (-1) AlleleSet-methods.Rd:51: Lost braces in \itemize; meant \describe ? checkRd: (-1) AlleleSet-methods.Rd:52: Lost braces in \itemize; meant \describe ? checkRd: (-1) AlleleSet-methods.Rd:53: Lost braces in \itemize; meant \describe ? checkRd: (-1) AlleleSet-methods.Rd:54: Lost braces in \itemize; meant \describe ? checkRd: (-1) AlleleSet-methods.Rd:55: Lost braces in \itemize; meant \describe ? checkRd: (-1) AlleleSet-methods.Rd:56: Lost braces in \itemize; meant \describe ? checkRd: (5) BeadStudioSet-class.Rd:52: \item in \describe must have non-empty label checkRd: (5) BeadStudioSet-class.Rd:53-54: \item in \describe must have non-empty label checkRd: (5) BeadStudioSet-class.Rd:55-57: \item in \describe must have non-empty label checkRd: (5) BeadStudioSet-class.Rd:58: \item in \describe must have non-empty label checkRd: (5) BeadStudioSet-class.Rd:59-60: \item in \describe must have non-empty label checkRd: (5) BeadStudioSet-class.Rd:63: \item in \describe must have non-empty label checkRd: (5) BeadStudioSet-class.Rd:64-65: \item in \describe must have non-empty label checkRd: (5) BeadStudioSet-class.Rd:66-67: \item in \describe must have non-empty label checkRd: (5) BeadStudioSet-class.Rd:68: \item in \describe must have non-empty label checkRd: (5) BeadStudioSetList-class.Rd:44-58: \item in \describe must have non-empty label checkRd: (5) BeadStudioSetList-class.Rd:64-69: \item in \describe must have non-empty label checkRd: (5) BeadStudioSetList-class.Rd:71-78: \item in \describe must have non-empty label checkRd: (5) CNSet-class.Rd:85-86: \item in \describe must have non-empty label checkRd: (5) CNSet-class.Rd:88-89: \item in \describe must have non-empty label checkRd: (5) CNSet-class.Rd:91-93: \item in \describe must have non-empty label checkRd: (5) CNSet-class.Rd:96-98: \item in \describe must have non-empty label checkRd: (5) CNSet-class.Rd:100-101: \item in \describe must have non-empty label checkRd: (5) CNSet-class.Rd:103-105: \item in \describe must have non-empty label checkRd: (5) CNSet-class.Rd:107: \item in \describe must have non-empty label checkRd: (5) CNSet-class.Rd:109: \item in \describe must have non-empty label checkRd: (5) CNSet-class.Rd:113: \item in \describe must have non-empty label checkRd: (5) CNSet-class.Rd:115-116: \item in \describe must have non-empty label checkRd: (5) CNSet-class.Rd:118: \item in \describe must have non-empty label checkRd: (5) CNSet-class.Rd:120-121: \item in \describe must have non-empty label checkRd: (5) CNSet-class.Rd:124-126: \item in \describe must have non-empty label checkRd: (5) CNSet-class.Rd:131-132: \item in \describe must have non-empty label checkRd: (5) CNSet-class.Rd:135-136: \item in \describe must have non-empty label checkRd: (5) CNSet-class.Rd:138: \item in \describe must have non-empty label checkRd: (5) CNSet-class.Rd:140-142: \item in \describe must have non-empty label checkRd: (5) CNSet-class.Rd:144-145: \item in \describe must have non-empty label checkRd: (5) CNSet-class.Rd:147-148: \item in \describe must have non-empty label checkRd: (5) CNSet-class.Rd:150-151: \item in \describe must have non-empty label checkRd: (5) CNSet-class.Rd:153: \item in \describe must have non-empty label checkRd: (5) GRanges-methods.Rd:28-38: \item in \describe must have non-empty label checkRd: (5) GRanges-methods.Rd:49-60: \item in \describe must have non-empty label checkRd: (5) GRanges-methods.Rd:62-67: \item in \describe must have non-empty label checkRd: (5) GRanges-methods.Rd:69-75: \item in \describe must have non-empty label checkRd: (5) GRanges-methods.Rd:77-85: \item in \describe must have non-empty label checkRd: (5) GenomeAnnotatedDataFrame-class.Rd:35-42: \item in \describe must have non-empty label checkRd: (5) GenomeAnnotatedDataFrame-class.Rd:44-54: \item in \describe must have non-empty label checkRd: (5) GenomeAnnotatedDataFrame-class.Rd:56-61: \item in \describe must have non-empty label checkRd: (5) GenomeAnnotatedDataFrame-class.Rd:68-73: \item in \describe must have non-empty label checkRd: (5) GenomeAnnotatedDataFrame-class.Rd:75-81: \item in \describe must have non-empty label checkRd: (5) GenomeAnnotatedDataFrame-class.Rd:84-89: \item in \describe must have non-empty label checkRd: (5) GenomeAnnotatedDataFrame-class.Rd:91-100: \item in \describe must have non-empty label checkRd: (5) SnpSet2-class.Rd:55-60: \item in \describe must have non-empty label checkRd: (5) SnpSet2-class.Rd:62-67: \item in \describe must have non-empty label checkRd: (5) SnpSet2-class.Rd:69-73: \item in \describe must have non-empty label checkRd: (5) chromosome-methods.Rd:44-45: \item in \describe must have non-empty label checkRd: (5) gSet-class.Rd:43-44: \item in \describe must have non-empty label checkRd: (5) gSet-class.Rd:45-46: \item in \describe must have non-empty label checkRd: (5) gSet-class.Rd:47-49: \item in \describe must have non-empty label checkRd: (5) gSet-class.Rd:50-52: \item in \describe must have non-empty label checkRd: (5) gSet-class.Rd:53-59: \item in \describe must have non-empty label checkRd: (5) gSet-class.Rd:61-66: \item in \describe must have non-empty label checkRd: (5) gSet-class.Rd:69-70: \item in \describe must have non-empty label checkRd: (5) gSet-class.Rd:72-77: \item in \describe must have non-empty label checkRd: (5) gSet-class.Rd:79-80: \item in \describe must have non-empty label checkRd: (5) gSet-class.Rd:81-86: \item in \describe must have non-empty label checkRd: (5) gSetList-class.Rd:51-56: \item in \describe must have non-empty label checkRd: (5) gSetList-class.Rd:58-64: \item in \describe must have non-empty label checkRd: (5) gSetList-class.Rd:66-71: \item in \describe must have non-empty label checkRd: (5) gSetList-class.Rd:74-79: \item in \describe must have non-empty label checkRd: (5) gSetList-class.Rd:89-99: \item in \describe must have non-empty label checkRd: (5) oligoSnpSet-methods.Rd:28-39: \item in \describe must have non-empty label checkRd: (5) oligoSnpSet-methods.Rd:41-46: \item in \describe must have non-empty label checkRd: (5) oligoSnpSet-methods.Rd:48-54: \item in \describe must have non-empty label * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: AlleleSet-class.Rd: eSet-class, VersionedBiobase-class, Versioned-class AssayDataList.Rd: assayDataNew BeadStudioSet-class.Rd: eSet-class, VersionedBiobase-class, Versioned-class CopyNumberSet-class.Rd: eSet-class, VersionedBiobase-class, Versioned-class GRanges-methods.Rd: GRanges-class GenomeAnnotatedDataFrame-class.Rd: AnnotatedDataFrame-class, Versioned-class GenomeAnnotatedDataFrameFrom-methods.Rd: AssayData SnpSet-methods.Rd: SnpSet, snpCallProbability SnpSet2-class.Rd: eSet-class, VersionedBiobase-class, Versioned-class, SnpSet-class SnpSuperSet-class.Rd: SnpSet-class, eSet-class, VersionedBiobase-class, Versioned-class SummarizedExperiment-methods.Rd: RangedSummarizedExperiment, RangedSummarizedExperiment-class gSet-class.Rd: eSet-class, VersionedBiobase-class, Versioned-class makeFeatureGRanges.Rd: findOverlaps, GRanges-class Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * checking for missing documentation entries ... WARNING Undocumented S4 methods: generic '[' and siglist 'CNSet,ANY,ANY,ANY' generic '[' and siglist 'gSetList,ANY,ANY,ANY' All user-level objects in a package (including S4 classes and methods) should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * 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 line endings in Makefiles ... OK * checking for GNU extensions in Makefiles ... OK * checking include directives in Makefiles ... OK * checking files in ‘vignettes’ ... WARNING Files in the 'vignettes' directory but no files in 'inst/doc': ‘scriptsForExampleData/CreateExampleData.R’ Package has no Sweave vignette sources and no VignetteBuilder field. * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘doRUnit.R’ OK * checking package vignettes ... NOTE Package has ‘vignettes’ subdirectory but apparently no vignettes. Perhaps the ‘VignetteBuilder’ information is missing from the DESCRIPTION file? * checking PDF version of manual ... OK * DONE Status: 3 WARNINGs, 4 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/oligoClasses.Rcheck/00check.log’ for details.