##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:scuttle.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings scuttle_1.17.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/scuttle.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 ‘scuttle/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scuttle’ version ‘1.17.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ‘scuttle’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* 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 ... 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 ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  addPerCellQCMetrics.Rd: SummarizedExperiment-class, rowData, colData
  aggregateAcrossCells.Rd: colData, SingleCellExperiment-class,
    SummarizedExperiment-class, reducedDims, altExps, DataFrame-class,
    applySCE
  aggregateAcrossFeatures.Rd: SummarizedExperiment-class
  calculateAverage.Rd: SummarizedExperiment-class,
    SingleCellExperiment-class, BiocParallelParam-class,
    DelayedMatrix-class, sizeFactors
  calculateCPM.Rd: SummarizedExperiment-class,
    SingleCellExperiment-class
  calculateFPKM.Rd: SummarizedExperiment-class,
    SingleCellExperiment-class
  calculateTPM.Rd: SummarizedExperiment-class,
    SingleCellExperiment-class
  computePooledFactors.Rd: SummarizedExperiment-class,
    SingleCellExperiment-class, sizeFactors
  computeSpikeFactors.Rd: SingleCellExperiment-class, altExps, altExp,
    sizeFactors
  downsampleBatches.Rd: SummarizedExperiment-class, List-class
  downsampleMatrix.Rd: RealizationSink-class, dgCMatrix-class,
    DelayedMatrix-class
  fitLinearModel.Rd: BiocParallelParam-class
  geometricSizeFactors.Rd: SummarizedExperiment-class,
    SingleCellExperiment-class, BiocParallelParam-class,
    DelayedArray-class, sizeFactors
  librarySizeFactors.Rd: SummarizedExperiment-class,
    SingleCellExperiment-class, BiocParallelParam-class,
    DelayedArray-class, sizeFactors
  logNormCounts.Rd: SingleCellExperiment-class,
    SummarizedExperiment-class, BiocParallelParam-class, applySCE,
    sizeFactors
  makePerCellDF.Rd: SingleCellExperiment-class, altExp, rowData
  makePerFeatureDF.Rd: SingleCellExperiment-class
  medianSizeFactors.Rd: SummarizedExperiment-class,
    SingleCellExperiment-class, sizeFactors
  mockSCE.Rd: SingleCellExperiment-class, colData, altExps,
    SingleCellExperiment
  normalizeCounts.Rd: SingleCellExperiment-class,
    SummarizedExperiment-class, DelayedMatrix-class,
    BiocParallelParam-class, sizeFactors
  numDetectedAcrossCells.Rd: SummarizedExperiment-class,
    DataFrame-class, SingleCellExperiment-class, colData,
    BiocParallelParam-class
  numDetectedAcrossFeatures.Rd: SummarizedExperiment-class,
    BiocParallelParam-class
  perCellQCFilters.Rd: DataFrame-class
  perCellQCMetrics.Rd: SingleCellExperiment-class,
    SummarizedExperiment-class, BiocParallelParam-class,
    DataFrame-class
  perFeatureQCMetrics.Rd: SummarizedExperiment-class,
    SingleCellExperiment-class, BiocParallelParam-class,
    DataFrame-class
  quickPerCellQC.Rd: DataFrame-class, SummarizedExperiment-class,
    colData
  readSparseCounts.Rd: readMM
  sumCountsAcrossCells.Rd: SummarizedExperiment-class, DataFrame-class,
    SingleCellExperiment-class, colData, BiocParallelParam-class,
    colsum
  sumCountsAcrossFeatures.Rd: SummarizedExperiment-class,
    BiocParallelParam-class
  summarizeAssayByGroup.Rd: SummarizedExperiment-class,
    DataFrame-class, colData, BiocParallelParam-class
  uniquifyDataFrameByGroup.Rd: DataFrame-class, colData, DFrame-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 ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... 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
computePooledFactors 5.922  0.136   6.059
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/scuttle.Rcheck/00check.log’
for details.