############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:R453Plus1Toolbox.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings R453Plus1Toolbox_1.57.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/R453Plus1Toolbox.Rcheck’ * using R Under development (unstable) (2024-11-24 r87369) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (conda-forge gcc 14.2.0-1) 14.2.0 GNU Fortran (conda-forge gcc 14.2.0-1) 14.2.0 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘R453Plus1Toolbox/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘R453Plus1Toolbox’ version ‘1.57.0’ * 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 ‘R453Plus1Toolbox’ can be installed ... OK * used C compiler: ‘gcc (conda-forge gcc 14.2.0-1) 14.2.0’ * checking installed package size ... INFO installed size is 5.3Mb sub-directories of 1Mb or more: R 1.9Mb extdata 2.8Mb * checking package directory ... OK * checking ‘build’ 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 dependencies in R code ... NOTE 'library' or 'require' call to ‘BSgenome.Hsapiens.UCSC.hg19’ in package code. Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .annotateVariants_MapperSet: no visible binding for global variable ‘Hsapiens’ .ava2vcf: no visible binding for global variable ‘Hsapiens’ .detectBreakpoints: no visible binding for global variable ‘Hsapiens’ .getEnsemblInfo: no visible binding for global variable ‘cds_length’ .getEnsemblInfo: no visible binding for global variable ‘ensembl_transcript_id’ .getMutations: no visible binding for global variable ‘PatternStart’ .getMutations: no visible binding for global variable ‘PatternEnd’ .htmlReport: no visible binding for global variable ‘VarFreqForward’ .htmlReport: no visible binding for global variable ‘VarFreqReverse’ .plotVariants: no visible binding for global variable ‘mutation’ qualityReportSFF: no visible binding for '<<-' assignment to ‘tmp’ annotateVariants,MapperSet-BSgenome: no visible binding for global variable ‘Hsapiens’ annotateVariants,MapperSet-missing: no visible binding for global variable ‘Hsapiens’ ava2vcf,AVASet: no visible binding for global variable ‘Hsapiens’ detectBreakpoints,list: no visible binding for global variable ‘Hsapiens’ subset,AVASet: no visible binding for global variable ‘referenceSeqID’ Undefined global functions or variables: Hsapiens PatternEnd PatternStart VarFreqForward VarFreqReverse cds_length ensembl_transcript_id mutation referenceSeqID * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: AVASet-class.Rd: eSet-class, VersionedBiobase-class, Versioned-class Breakpoints-class.Rd: PairwiseAlignmentsSingleSubject-class, AlignedRead-class MapperSet-class.Rd: eSet-class, VersionedBiobase-class, Versioned-class alignShortReads.Rd: matchPDict, DNAStringSet, AlignedRead ava2vcf.Rd: VCF-class, writeVcf baseFrequency.Rd: DNAStringSet, ShortRead, alphabetFrequency baseQualityHist.Rd: QualityScaledDNAStringSet, ShortReadQ baseQualityStats.Rd: QualityScaledDNAStringSet, ShortReadQ complexity.dust.Rd: DNAStringSet, ShortRead complexity.entropy.Rd: DNAStringSet, ShortRead coverageOnTarget.Rd: scanBam demultiplexReads.Rd: DNAStringSet detectBreakpoints.Rd: scanBam, IRanges, PairwiseAlignmentsSingleSubject, AlignedRead dinucleotideOddsRatio.Rd: DNAStringSet, ShortRead featureDataAmp.Rd: AnnotatedDataFrame filterChimericReads.Rd: scanBam gcContent.Rd: DNAStringSet, ShortRead gcContentHist.Rd: DNAStringSet, ShortRead gcPerPosition.Rd: DNAStringSet, ShortRead getAlignedReads.Rd: DNAStringSet htmlReport.Rd: fData nucleotideCharts.Rd: DNAStringSet, ShortRead positionQualityBoxplot.Rd: QualityScaledDNAStringSet, ShortReadQ readLengthHist.Rd: DNAStringSet, ShortRead readLengthStats.Rd: DNAStringSet, ShortRead readsOnTarget.Rd: scanBam removeLinker.Rd: DNAStringSet, pairwiseAlignment sequenceQualityHist.Rd: QualityScaledDNAStringSet, ShortReadQ Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed mergeBreakpoints 7.062 0.055 7.152 * 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: 4 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/R453Plus1Toolbox.Rcheck/00check.log’ for details.