############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:adverSCarial.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings adverSCarial_1.3.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/adverSCarial.Rcheck’ * using R version 4.4.0 RC (2024-04-16 r86468) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘adverSCarial/DESCRIPTION’ ... OK * this is package ‘adverSCarial’ version ‘1.3.2’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘adverSCarial’ 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 ... NOTE .advModificationsFunction: no visible global function definition for ‘is’ .advModificationsFunction : : no visible global function definition for ‘is’ .advModificationsNotFunction: no visible global function definition for ‘is’ .advModificationsNotFunction: no visible global function definition for ‘counts’ .advModificationsNotFunction : : no visible global function definition for ‘is’ .randWalkGetSeed: no visible global function definition for ‘SingleCellExperiment’ .randWalkGetSeed: no visible global function definition for ‘is’ .randWalkTryNewVector: no visible global function definition for ‘SingleCellExperiment’ .randWalkTryNewVector: no visible global function definition for ‘is’ MClassifier: no visible global function definition for ‘is’ MClassifier: no visible global function definition for ‘counts’ advChar: no visible global function definition for ‘new’ advGridMinChange: no visible global function definition for ‘is’ advGridMinChange: no visible global function definition for ‘counts’ advGridMinChange: no visible global function definition for ‘SingleCellExperiment’ advList: no visible global function definition for ‘new’ advMaxChange: no visible global function definition for ‘is’ advMaxChange: no visible global function definition for ‘counts’ advMaxChange: no visible global function definition for ‘new’ advModifications: no visible global function definition for ‘is’ advModifications: no visible global function definition for ‘counts’ advModifications: no visible global function definition for ‘SingleCellExperiment’ advRandWalkMinChange: no visible global function definition for ‘is’ advRandWalkMinChange: no visible global function definition for ‘counts’ advSingleGene: no visible global function definition for ‘is’ advSingleGene: no visible global function definition for ‘counts’ advSingleGene: no visible binding for '<<-' assignment to ‘lastResLength’ advSingleGene : : no visible binding for global variable ‘lastResLength’ advSingleGene : : no visible binding for '<<-' assignment to ‘lastResLength’ advSingleGene: no visible global function definition for ‘new’ getDistantCouples: no visible global function definition for ‘combn’ getSignGenes : : no visible global function definition for ‘wilcox.test’ getSignGenes : : no visible global function definition for ‘t.test’ matrixFromSCE: no visible global function definition for ‘is’ matrixFromSCE: no visible global function definition for ‘colData’ maxChangeOverview: no visible global function definition for ‘is’ maxChangeOverview: no visible global function definition for ‘counts’ predictWithNewValue: no visible global function definition for ‘is’ sceConvertToHGNC: no visible global function definition for ‘is’ sceConvertToHGNC: no visible global function definition for ‘SingleCellExperiment’ sceConvertToHGNC: no visible global function definition for ‘colData’ singleGeneOverview: no visible global function definition for ‘is’ singleGeneOverview: no visible global function definition for ‘counts’ Undefined global functions or variables: SingleCellExperiment colData combn counts is lastResLength new t.test wilcox.test Consider adding importFrom("methods", "is", "new") importFrom("stats", "t.test", "wilcox.test") importFrom("utils", "combn") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * checking Rd files ... NOTE checkRd: (-1) advGridMinChange.Rd:34-37: Lost braces 34 | classifier = function(expr, clusters, target){ | ^ checkRd: (-1) advIGD4C.Rd:31-34: Lost braces 31 | classifier = function(expr, clusters, target){ | ^ checkRd: (-1) advMaxChange.Rd:39-42: Lost braces 39 | classifier = function(expr, clusters, target){ | ^ checkRd: (-1) advRandWalkMinChange.Rd:36-39: Lost braces 36 | classifier = function(expr, clusters, target){ | ^ checkRd: (-1) advSingleGene.Rd:43-46: Lost braces 43 | classifier = function(expr, clusters, target){ | ^ checkRd: (-1) maxChangeOverview.Rd:35-38: Lost braces 35 | classifier = function(expr, clusters, target){ | ^ checkRd: (-1) predictWithNewValue.Rd:36-39: Lost braces 36 | classifier = function(expr, clusters, target){ | ^ checkRd: (-1) singleGeneOverview.Rd:37-40: Lost braces 37 | classifier = function(expr, clusters, target){ | ^ * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Undocumented code objects: ‘advTraining’ All user-level objects in a package should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... WARNING Undocumented arguments in Rd file 'advMaxChange.Rd' ‘slot’ Undocumented arguments in Rd file 'advModifications.Rd' ‘slot’ Undocumented arguments in Rd file 'advSingleGene.Rd' ‘slot’ Undocumented arguments in Rd file 'predictWithNewValue.Rd' ‘slot’ 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’ ... NOTE The following directory looks like a leftover from 'knitr': ‘figure’ Please remove from your package. * checking examples ... ERROR Running examples in ‘adverSCarial-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: MClassifier > ### Title: Example cell type classifier for pbmc clustered datasets. > ### Aliases: MClassifier > > ### ** Examples > > library(TENxPBMCData) 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, table, tapply, union, 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: 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 Loading required package: HDF5Array Loading required package: SparseArray 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: DelayedArray Attaching package: ‘DelayedArray’ The following objects are masked from ‘package:base’: apply, scale, sweep Loading required package: rhdf5 Attaching package: ‘HDF5Array’ The following object is masked from ‘package:rhdf5’: h5ls > > pbmc <- TENxPBMCData(dataset = "pbmc3k") see ?TENxPBMCData and browseVignettes('TENxPBMCData') for documentation loading from cache > mat_rna <- matrixFromSCE(pbmc) > cell_types <- system.file("extdata", + "pbmc3k_cell_types.tsv", + package = "adverSCarial" + ) > cell_types <- read.table(cell_types, sep = "\t")$cell_type > > MClassifier(mat_rna, cell_types, "DC") Error in `.rowNamesDF<-`(x, value = value) : invalid 'row.names' length Calls: MClassifier ... row.names<- -> row.names<-.data.frame -> .rowNamesDF<- Execution halted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.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 ERROR, 2 WARNINGs, 3 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/adverSCarial.Rcheck/00check.log’ for details.