##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:scDblFinder.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings scDblFinder_1.13.6.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/scDblFinder.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 10.4.0
    GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'scDblFinder/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'scDblFinder' version '1.13.6'
* 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 ... OK
* checking for portable file names ... OK
* checking whether package 'scDblFinder' 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 R 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 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
plotThresholds: no visible binding for global variable 'threshold'
plotThresholds: no visible binding for global variable 'value'
plotThresholds: no visible binding for global variable 'variable'
Undefined global functions or variables:
  threshold value variable
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'aggregateFeatures':
aggregateFeatures
  Code: function(x, dims.use = seq(2L, 12L), k = 1000, num_init = 3,
                 use.mbk = NULL, use.subset = 5000, norm.fn = TFIDF,
                 twoPass = FALSE, ...)
  Docs: function(x, dims.use = seq(2L, 12L), k = 100, num_init = 3,
                 use.mbk = NULL, use.subset = 5000, norm.fn = TFIDF,
                 twoPass = FALSE, ...)
  Mismatches in argument default values:
    Name: 'k' Code: 1000 Docs: 100

Codoc mismatches from documentation object 'scDblFinder':
scDblFinder
  Code: function(sce, clusters = NULL, samples = NULL, clustCor = NULL,
                 artificialDoublets = NULL, knownDoublets = NULL,
                 knownUse = c("discard", "positive"), dbr = NULL,
                 dbr.sd = NULL, nfeatures = 1352, dims = 20, k = NULL,
                 removeUnidentifiable = TRUE, includePCs = 19,
                 propRandom = 0, propMarkers = 0, aggregateFeatures =
                 FALSE, returnType = c("sce", "table", "full",
                 "counts"), score = c("xgb", "weighted", "ratio"),
                 processing = "default", metric = "logloss", nrounds =
                 0.25, max_depth = 4, iter = 3, trainingFeatures =
                 NULL, unident.th = NULL, multiSampleMode = c("split",
                 "singleModel", "singleModelSplitThres", "asOne"),
                 threshold = TRUE, verbose = is.null(samples), BPPARAM
                 = SerialParam(), ...)
  Docs: function(sce, clusters = NULL, samples = NULL, clustCor = NULL,
                 artificialDoublets = NULL, knownDoublets = NULL,
                 knownUse = c("discard", "positive"), dbr = NULL,
                 dbr.sd = NULL, nfeatures = 1000, dims = 20, k = NULL,
                 removeUnidentifiable = TRUE, includePCs = 10,
                 propRandom = 0, propMarkers = 0, aggregateFeatures =
                 FALSE, returnType = c("sce", "table", "full",
                 "counts"), score = c("xgb", "weighted", "ratio"),
                 processing = "default", metric = "logloss", nrounds =
                 0.25, max_depth = 4, iter = 3, trainingFeatures =
                 NULL, unident.th = NULL, multiSampleMode = c("split",
                 "singleModel", "singleModelSplitThres", "asOne"),
                 threshold = TRUE, verbose = is.null(samples), BPPARAM
                 = SerialParam(), ...)
  Mismatches in argument default values:
    Name: 'nfeatures' Code: 1352 Docs: 1000
    Name: 'includePCs' Code: 19 Docs: 10

* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'aggregateFeatures'
  'norm.fn'
Documented arguments not in \usage in documentation object 'aggregateFeatures':
  'use.TFIDF'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
doubletThresholding 13.98   0.24   14.29
scDblFinder         12.50   0.31   12.84
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 1 NOTE
See
  'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/scDblFinder.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL scDblFinder
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library'
* installing *source* package 'scDblFinder' ...
** using staged installation
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (scDblFinder)

R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

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(scDblFinder)
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

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, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

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

    windows

Loading required package: GenomeInfoDb
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("scDblFinder")
[ FAIL 0 | WARN 8 | SKIP 0 | PASS 104 ]

[ FAIL 0 | WARN 8 | SKIP 0 | PASS 104 ]
> 
> proc.time()
   user  system elapsed 
  46.09    1.48   47.54