############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:SingleCellExperiment.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings SingleCellExperiment_1.29.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/SingleCellExperiment.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 ‘SingleCellExperiment/DESCRIPTION’ ... OK * this is package ‘SingleCellExperiment’ version ‘1.29.1’ * 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 ‘SingleCellExperiment’ 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 dependencies in R code ... NOTE Unexported objects imported by ':::' calls: ‘BiocGenerics:::replaceSlots’ ‘S4Vectors:::disableValidity’ ‘SummarizedExperiment:::.SummarizedExperiment.charbound’ 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 ... OK * 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: SingleCellExperiment.Rd: RangedSummarizedExperiment-class, SummarizedExperiment, SummarizedExperiment-class, SelfHits-class, assays, rowData, colData altExps.Rd: SummarizedExperiment-class, colData, List-class, assay<-, Annotated-class, metadata, Vector-class, mcols assays.Rd: assay, assay<- colLabels.Rd: SummarizedExperiment-class, colData colPairs.Rd: SelfHits-class, List-class, mcols combine.Rd: rbind,SummarizedExperiment-method, cbind,SummarizedExperiment-method, colData, combineCols,SummarizedExperiment-method, combineCols, [,SummarizedExperiment-method, SummarizedExperiment-class internals.Rd: DataFrame-class, rowData, colData, metadata, rowData,SummarizedExperiment-method, colData,SummarizedExperiment-method, rowData<-, colData<-, metadata<- reducedDims.Rd: List-class, assay<-, Annotated-class, metadata, Vector-class, mcols rowPairs.Rd: SelfHits-class, List-class, mcols rowSubset.Rd: rowData simplifyToSCE.Rd: SummarizedExperiment-class sizeFactors.Rd: colData unsplitAltExps.Rd: colData, ConstantMatrix-class, DelayedArray-class updateObject.Rd: sizeFactors<-, colData 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 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 running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/SingleCellExperiment.Rcheck/00check.log’ for details.