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### Running command:
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### /home/biocbuild/bbs-3.23-bioc-gpu/R/bin/R CMD check --install=check:scviR.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc-gpu/R/site-library --timings scviR_1.11.0.tar.gz
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* using log directory ‘/media/volume/biocgpu2/biocbuild/bbs-3.23-bioc-gpu/meat/scviR.Rcheck’
* using R Under development (unstable) (2025年11月17日 r89032)
* 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 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘scviR/DESCRIPTION’ ... OK
* this is package ‘scviR’ version ‘1.11.0’
* package encoding: UTF-8
* 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 ... NOTE
Found the following hidden files and directories:
 .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘scviR’ 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 ... 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 ... OK
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
 user system elapsed
muonR 5.129 1.195 6.468
getSubclLM 5.398 0.712 6.118
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
 Running ‘test.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 NOTE
See
 ‘/media/volume/biocgpu2/biocbuild/bbs-3.23-bioc-gpu/meat/scviR.Rcheck/00check.log’
for details.

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### Running command:
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### /home/biocbuild/bbs-3.23-bioc-gpu/R/bin/R CMD INSTALL scviR
###
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* installing to library ‘/media/volume/biocgpu2/biocbuild/bbs-3.23-bioc-gpu/R/site-library’
* installing *source* package ‘scviR’ ...
** this is package ‘scviR’ version ‘1.11.0’
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (scviR)

R Under development (unstable) (2025年11月17日 r89032) -- "Unsuffered Consequences"
Copyright (C) 2025 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(scviR)
Loading required package: basilisk
Loading required package: reticulate
Loading required package: shiny
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("scviR")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 2 ]
> 
> proc.time()
 user system elapsed 
 11.567 0.587 12.158