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### Running command:
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###   /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD check --install=check:SingleCellExperiment.install-out.txt --library=/home/rapidbuild/bbs-3.21-bioc-rapid/R/site-library --timings SingleCellExperiment_1.29.1.tar.gz
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* using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/SingleCellExperiment.Rcheck’
* using R Under development (unstable) (2024-11-14 r87333)
* 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 ‘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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/SingleCellExperiment.Rcheck/00check.log’
for details.