############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:easyRNASeq.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings easyRNASeq_2.43.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/easyRNASeq.Rcheck’ * using R Under development (unstable) (2025-01-20 r87609) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.2 LTS * using session charset: UTF-8 * checking for file ‘easyRNASeq/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘easyRNASeq’ version ‘2.43.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Files named as vignettes but with no recognized vignette engine: ‘inst/doc/01-Introduction.Rmd’ ‘inst/doc/02-AnnotParam.Rmd’ ‘inst/doc/03-SyntheticTranscripts.Rmd’ ‘inst/doc/04-BamParam.Rmd’ ‘inst/doc/05-RnaSeqParam.Rmd’ ‘inst/doc/06-simpleRNASeq.Rmd’ ‘inst/doc/07-cleanUp.Rmd’ ‘inst/doc/08-Session-Info.Rmd’ ‘inst/doc/09-Acknowledgments.Rmd’ ‘inst/doc/10-Foonotes.Rmd’ ‘inst/doc/11-Images.Rmd’ ‘inst/doc/12-Appendix.Rmd’ (Is a VignetteBuilder field missing?) * 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 ‘easyRNASeq’ can be installed ... OK * checking installed package size ... OK * 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 whether startup messages can be suppressed ... 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) easyRNASeq-AnnotParam.Rd:40-43: Lost braces in \itemize; meant \describe ? checkRd: (-1) easyRNASeq-AnnotParam.Rd:44-51: Lost braces in \itemize; meant \describe ? checkRd: (-1) easyRNASeq-RnaSeqParam-class.Rd:14: Lost braces in \itemize; meant \describe ? checkRd: (-1) easyRNASeq-RnaSeqParam-class.Rd:15: Lost braces in \itemize; meant \describe ? checkRd: (-1) easyRNASeq-annotation-methods.Rd:25: Lost braces in \itemize; meant \describe ? checkRd: (-1) easyRNASeq-annotation-methods.Rd:26: Lost braces in \itemize; meant \describe ? checkRd: (-1) easyRNASeq-correction-methods.Rd:48-50: Lost braces in \itemize; meant \describe ? checkRd: (-1) easyRNASeq-correction-methods.Rd:51-54: Lost braces in \itemize; meant \describe ? checkRd: (-1) easyRNASeq-datasets.Rd:11-21: Lost braces in \itemize; meant \describe ? checkRd: (-1) easyRNASeq-internal-AnnotParam-methods.Rd:25: Lost braces 25 | These are \code{\linkS4class{AnnotParam}}{AnnotParam} class internal methods: | ^ checkRd: (-1) easyRNASeq-package.Rd:109-112: Lost braces in \itemize; meant \describe ? checkRd: (-1) easyRNASeq-package.Rd:113-121: Lost braces in \itemize; meant \describe ? * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Non-topic package-anchored link(s) in Rd file 'GenomicRanges-methods.Rd': ‘[BiocGenerics]{row_colnames}’ Non-topic package-anchored link(s) in Rd file 'easyRNASeq-AnnotParam-accessors.Rd': ‘[easyRNASeq:easyRNASeq-AnnotParam-class]{AnnotParam}’ Non-topic package-anchored link(s) in Rd file 'easyRNASeq-AnnotParam-class.Rd': ‘[easyRNASeq:easyRNASeq-AnnotParam]{AnnotParam}’ ‘[easyRNASeq:easyRNASeq-RnaSeqParam]{RnaSeqParam constructor}’ ‘[easyRNASeq:easyRNASeq-RnaSeqParam-accessors]{RnaSeqParam accessors}’ ‘[easyRNASeq:easyRNASeq-simpleRNASeq]{simpleRNASeq function}’ ‘[easyRNASeq:easyRNASeq-AnnotParam]{AnnotParam constructor}’ Non-topic package-anchored link(s) in Rd file 'easyRNASeq-AnnotParam.Rd': ‘[easyRNASeq:easyRNASeq-annotation-methods]{getAnnotation}’ Non-topic package-anchored link(s) in Rd file 'easyRNASeq-BamParam-accessors.Rd': ‘[easyRNASeq:easyRNASeq-BamParam-class]{BamParam}’ ‘[easyRNASeq:easyRNASeq-RnaSeqParam-accessors]{RnaSeqParam yieldSize}’ Non-topic package-anchored link(s) in Rd file 'easyRNASeq-BamParam-class.Rd': ‘[easyRNASeq:easyRNASeq-BamParam-accessors]{BamParam accessors}’ ‘[easyRNASeq:easyRNASeq-RnaSeqParam]{RnaSeqParam constructor}’ ‘[easyRNASeq:easyRNASeq-RnaSeqParam-accessors]{RnaSeqParam accessors}’ ‘[easyRNASeq:easyRNASeq-simpleRNASeq]{simpleRNASeq function}’ ‘[easyRNASeq:easyRNASeq-AnnotParam]{AnnotParam constructor}’ Non-topic package-anchored link(s) in Rd file 'easyRNASeq-RnaSeqParam-accessors.Rd': ‘[easyRNASeq:easyRNASeq-AnnotParam-class]{AnnotParam}’ ‘[easyRNASeq:easyRNASeq-BamParam-class]{BamParam}’ ‘[easyRNASeq:easyRNASeq-RnaSeqParam-class]{RnaSeqParam}’ ‘[easyRNASeq:easyRNASeq-BamParam-accessors]{BamParam yieldSize}’ Non-topic package-anchored link(s) in Rd file 'easyRNASeq-RnaSeqParam-class.Rd': ‘[easyRNASeq:easyRNASeq-simpleRNASeq]{simpleRNASeq function}’ ‘[easyRNASeq:easyRNASeq-summarization-methods]{easyRNASeq summarization functions}’ ‘[easyRNASeq:easyRNASeq-RnaSeqParam]{RnaSeqParam constructor}’ ‘[easyRNASeq:easyRNASeq-RnaSeqParam-accessors]{RnaSeqParam accessors}’ ‘[easyRNASeq:easyRNASeq-AnnotParam]{AnnotParam constructor}’ ‘[easyRNASeq:easyRNASeq-BamParam]{BamParam constructor}’ Non-topic package-anchored link(s) in Rd file 'easyRNASeq-annotation-methods.Rd': ‘[genomeIntervals]{genomeIntervals-readGff3}’ ‘[easyRNASeq:easyRNASeq-annotation-internal-methods]{readGffGtf}’ Non-topic package-anchored link(s) in Rd file 'easyRNASeq-class.Rd': ‘[easyRNASeq:easyRNASeq-easyRNASeq]{easyRNASeq}’ ‘[easyRNASeq:easyRNASeq-accessors]{easyRNASeq accessors}’ ‘[easyRNASeq:easyRNASeq-annotation-methods]{easyRNASeq annotation}’ ‘[easyRNASeq:easyRNASeq-correction-methods]{easyRNASeq correction (FPKM)}’ ‘[easyRNASeq:easyRNASeq-coverage-methods]{easyRNASeq coverage}’ ‘[easyRNASeq:easyRNASeq-summarization-methods]{easyRNASeq summarization}’ ‘[easyRNASeq:print-methods]{easyRNASeq print methods}’ Non-topic package-anchored link(s) in Rd file 'easyRNASeq-correction-methods.Rd': ‘[easyRNASeq:easyRNASeq-accessors]{readCounts}’ Non-topic package-anchored link(s) in Rd file 'easyRNASeq-defunct-annotation-methods.Rd': ‘[easyRNASeq:easyRNASeq-annotation-methods]{getAnnotation}’ Non-topic package-anchored link(s) in Rd file 'easyRNASeq-defunct.Rd': ‘[easyRNASeq:easyRNASeq-easyRNASeq]{easyRNASeq}’ ‘[easyRNASeq:easyRNASeq-coverage-methods]{fetchCoverage}’ ‘[easyRNASeq:easyRNASeq-simpleRNASeq]{simpleRNASeq}’ Non-topic package-anchored link(s) in Rd file 'easyRNASeq-easyRNASeq.Rd': ‘[easyRNASeq:ShortRead-methods]{use ShortRead/Rsamtools methods}’ ‘[easyRNASeq:easyRNASeq-annotation-methods]{fetch the annotations}’ ‘[easyRNASeq:easyRNASeq-coverage-methods]{get the reads coverage}’ ‘[easyRNASeq:easyRNASeq-summarization-methods]{summarize the reads}’ ‘[easyRNASeq:easyRNASeq-correction-methods]{optionally apply}’ ‘[easyRNASeq:edgeR-methods]{use edgeR methods}’ ‘[easyRNASeq:easyRNASeq-annotation-internal-methods]{readGffGtf}’ Non-topic package-anchored link(s) in Rd file 'easyRNASeq-global-variables.Rd': ‘[base:ns-hooks]{.onAttach}’ Non-topic package-anchored link(s) in Rd file 'easyRNASeq-package.Rd': ‘[easyRNASeq:easyRNASeq-easyRNASeq]{easyRNASeq}’ ‘[easyRNASeq:ShortRead-methods]{ShortRead methods}’ ‘[easyRNASeq:easyRNASeq-annotation-methods]{easyRNASeq annotation methods}’ ‘[easyRNASeq:easyRNASeq-coverage-methods]{easyRNASeq coverage methods}’ ‘[easyRNASeq:easyRNASeq-summarization-methods]{easyRNASeq summarization methods}’ ‘[easyRNASeq:easyRNASeq-correction-methods]{easyRNASeq correction methods}’ ‘[easyRNASeq:edgeR-methods]{edgeR methods}’ Non-topic package-anchored link(s) in Rd file 'easyRNASeq-simpleRNASeq.Rd': ‘[easyRNASeq:easyRNASeq-easyRNASeq]{easyRNASeq}’ ‘[easyRNASeq:easyRNASeq-annotation-methods]{annotations}’ ‘[easyRNASeq:easyRNASeq-summarization-methods]{summarizes}’ ‘[easyRNASeq:easyRNASeq-BamFileList]{getBamFileList}’ Non-topic package-anchored link(s) in Rd file 'easyRNASeq-summarization-internal-methods.Rd': ‘[easyRNASeq:easyRNASeq-easyRNASeq]{easyRNASeq}’ Non-topic package-anchored link(s) in Rd file 'easyRNASeq-summarization-methods.Rd': ‘[easyRNASeq:easyRNASeq-annotation-methods]{easyRNASeq annotation methods}’ ‘[easyRNASeq:easyRNASeq-summarization-internal-methods]{.geneModelSummarization}’ ‘[easyRNASeq:easyRNASeq-island-methods]{findIslands}’ Non-topic package-anchored link(s) in Rd file 'genomeIntervals-methods.Rd': ‘[genomeIntervals]{genomeIntervals-readGff3}’ See section 'Cross-references' in the 'Writing R Extensions' manual. Found the following Rd file(s) with Rd \link{} targets missing package anchors: BiocFileCache-methods.Rd: BiocFileCache-class GenomicRanges-methods.Rd: GRangesList-class, GAlignments-class, DataFrame-class IRanges-methods.Rd: IRangesList-class Rsamtools-methods.Rd: BamFile-class ShortRead-methods.Rd: AlignedRead-class, SRFilter-class basename-methods.Rd: BamFile-class easyRNASeq-annotation-internal-methods.Rd: Genome_intervals_stranded-class easyRNASeq-class.Rd: GRangesList-class, RleList-class easyRNASeq-coverage-methods.Rd: Rle-class easyRNASeq-easyRNASeq.Rd: GRangesList-class easyRNASeq-simpleRNASeq.Rd: BamFile-class edgeR-methods.Rd: DGEList-class file.exists-methods.Rd: BamFile-class genomeIntervals-methods.Rd: Genome_intervals-class 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 ... WARNING Documented arguments not in \usage in Rd file 'easyRNASeq-annotation-internal-methods.Rd': ‘annotation.type’ ‘fields’ ‘filename’ ‘format’ ‘gAnnot’ ‘nbCore’ Objects in \usage without \alias in Rd file 'easyRNASeq-coverage-methods.Rd': ‘\S4method{fetchCoverage}{RNAseq}’ Documented arguments not in \usage in Rd file 'easyRNASeq-internal-AnnotParam-methods.Rd': ‘...’ Documented arguments not in \usage in Rd file 'easyRNASeq-internal-methods.Rd': ‘arg’ ‘chr.names’ ‘fun’ ‘organism’ ‘type’ ‘value’ ‘x’ ‘...’ Documented arguments not in \usage in Rd file 'easyRNASeq-summarization-internal-methods.Rd': ‘chr.map’ ‘chr.sel’ ‘cList’ ‘count’ ‘filename’ ‘filter’ ‘format’ ‘gapped’ ‘min.cov’ ‘min.length’ ‘max.gap’ ‘plot’ ‘rnaSeq’ ‘summarization’ ‘silent’ ‘subType’ ‘type’ ‘validity.check’ ‘values’ ‘...’ Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * 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’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed easyRNASeq-simpleRNASeq 72.033 2.969 77.078 easyRNASeq-package 47.838 2.369 50.869 easyRNASeq-synthetic-transcripts 37.559 1.791 39.386 BiocFileCache-methods 9.126 1.039 20.260 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.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: 1 WARNING, 2 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/easyRNASeq.Rcheck/00check.log’ for details.