############################################################################## ############################################################################## ### ### 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.