##############################################################################
##############################################################################
###
### Running command:
###
###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/R CMD check --install=check:scuttle.install-out.txt --library=/home/rapidbuild/bbs-3.23-bioc-rapid/R/site-library --timings scuttle_1.21.6.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/scuttle.Rcheck’
* using R version 4.6.0 alpha (2026-04-04 r89791)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-04-13 19:29:27 UTC
* checking for file ‘scuttle/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scuttle’ version ‘1.21.6’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>’

Unknown, possibly misspelled, fields in DESCRIPTION:
  ‘git_url’ ‘git_branch’ ‘git_last_commit’ ‘git_last_commit_date’
* 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 ‘scuttle’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
* checking C++ specification ... INFO
  specified C++17
* checking installed package size ... INFO
  installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
* 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 use of S3 registration ... 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 ... NOTE
downsampleMatrix: warning in downsample_column(initializeCpp(x), prop =
  rep(prop, length.out = ncol(x)), already_integer = input.integer,
  output_sparse = as.sparse, output_integer = as.integer): partial
  argument match of 'prop' to 'prop_col'
downsampleMatrix: warning in downsample_global(initializeCpp(x), prop =
  prop, already_integer = input.integer, output_sparse = as.sparse,
  output_integer = as.integer, num_threads = num.threads): partial
  argument match of 'prop' to 'prop_global'
* 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
  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 ... INFO
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... WARNING
Found the following significant warnings:

  Warning in .local(x, ...) : 'aggregateAcrossCells' is deprecated.
  Warning in .local(x, ...) : 'aggregateAcrossCells' is deprecated.
  Warning in .local(x, ...) : 'aggregateAcrossCells' is deprecated.
  Warning in .local(x, ...) : 'aggregateAcrossCells' is deprecated.
  Warning in .local(x, ...) : 'aggregateAcrossCells' is deprecated.
  Warning in .local(x, ...) : 'librarySizeFactors' is deprecated.
  Warning in .local(x, ...) : 'librarySizeFactors' is deprecated.
  Warning in .local(x, ...) : 'summarizeAssayByGroup' is deprecated.
  Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
  Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
  Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
  Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
  Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
  Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
  Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
  Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
  Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
  Warning in .local(x, ...) : 'librarySizeFactors' is deprecated.
  Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
  Warning in .local(x, ...) : 'librarySizeFactors' is deprecated.
  Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
  Warning in .local(x, ...) : 'librarySizeFactors' is deprecated.
  Warning in .local(x, ...) : 'normalizeCounts' is deprecated.
  Warning in .local(x, ...) : 'summarizeAssayByGroup' is deprecated.
  Warning in .local(x, ...) : 'quickPerCellQC' is deprecated.
  Warning in .local(x, ...) : 'summarizeAssayByGroup' is deprecated.
  Warning in .local(x, ...) : 'summarizeAssayByGroup' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
* 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: 1 WARNING, 3 NOTEs
See
  ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/scuttle.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/R CMD INSTALL scuttle
###
##############################################################################
##############################################################################


* installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library’
* installing *source* package ‘scuttle’ ...
** this is package ‘scuttle’ version ‘1.21.6’
** using staged installation
** libs
specified C++17
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
using C++17
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I../inst/include/ -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/assorthead/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I../inst/include/ -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/assorthead/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c aggregate_across_cells.cpp -o aggregate_across_cells.o
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I../inst/include/ -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/assorthead/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c cumulative_prop.cpp -o cumulative_prop.o
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I../inst/include/ -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/assorthead/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c downsample_counts.cpp -o downsample_counts.o
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I../inst/include/ -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/assorthead/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c fit_linear_model.cpp -o fit_linear_model.o
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I../inst/include/ -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/assorthead/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c pool_size_factors.cpp -o pool_size_factors.o
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I../inst/include/ -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/assorthead/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c set_executor.cpp -o set_executor.o
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I../inst/include/ -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/assorthead/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c sum_counts.cpp -o sum_counts.o
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG -I../inst/include/ -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/beachmat/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/assorthead/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c utils.cpp -o utils.o
g++ -std=gnu++17 -shared -L/usr/local/lib -o scuttle.so RcppExports.o aggregate_across_cells.o cumulative_prop.o downsample_counts.o fit_linear_model.o pool_size_factors.o set_executor.o sum_counts.o utils.o -llapack -L/home/rapidbuild/bbs-3.23-bioc-rapid/R/lib -lRblas -lgfortran -lm -lquadmath
installing to /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/00LOCK-scuttle/00new/scuttle/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (scuttle)

R version 4.6.0 alpha (2026-04-04 r89791)
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(scuttle)
Loading required package: SingleCellExperiment
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: Seqinfo
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians

> test_check("scuttle")
Loading required package: Matrix

Attaching package: 'Matrix'

The following object is masked from 'package:S4Vectors':

    expand

Loading required package: S4Arrays
Loading required package: abind

Attaching package: 'S4Arrays'

The following object is masked from 'package:abind':

    abind

The following object is masked from 'package:base':

    rowsum

Loading required package: SparseArray

Attaching package: 'DelayedArray'

The following objects are masked from 'package:base':

    apply, scale, sweep

[ FAIL 0 | WARN 542 | SKIP 0 | PASS 1733 ]

[ FAIL 0 | WARN 542 | SKIP 0 | PASS 1733 ]
Warning messages:
1: In .library_size_factors(assay(x, assay.type), ...) :
  'librarySizeFactors' is deprecated.
Use 'scrapper::centerSizeFactors' instead.
See help("Deprecated")
2: In .local(x, ...) : 'normalizeCounts' is deprecated.
Use 'scrapper::normalizeCounts' instead.
See help("Deprecated")
> 
> proc.time()
   user  system elapsed 
 70.703   1.006  71.698