* using log directory ‘/srv/hornik/tmp/CRAN_pretest/RCNA.Rcheck’ * using R Under development (unstable) (2024-11-19 r87348) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 19.1.1 (1) Debian flang-new version 19.1.1 (1) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘RCNA/DESCRIPTION’ ... OK * this is package ‘RCNA’ version ‘0.1’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [2s/2s] NOTE Maintainer: ‘Matt Bradley ’ New submission Non-FOSS package license (GPLv3) Possibly misspelled words in DESCRIPTION: RCNA (2:49, 5:55) * 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 executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘RCNA’ can be installed ... [3s/3s] WARNING Found the following significant warnings: Warning: replacing previous import ‘R.utils::timestamp’ by ‘utils::timestamp’ when loading ‘RCNA’ See ‘/srv/hornik/tmp/CRAN_pretest/RCNA.Rcheck/00install.out’ for details. * checking package directory ... OK * checking for future file timestamps ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences. Non-standard license specification: GPLv3 Standardizable: FALSE * 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 ... [1s/1s] OK * checking whether the package can be loaded with stated dependencies ... [1s/1s] OK * checking whether the package can be unloaded cleanly ... [1s/1s] OK * checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK * checking whether the namespace can be unloaded cleanly ... [1s/1s] OK * checking loading without being on the library search path ... [1s/1s] OK * checking use of S3 registration ... OK * checking dependencies in R code ... WARNING 'library' or 'require' calls not declared from: ‘foreach’ ‘parallel’ 'library' or 'require' calls in package code: ‘foreach’ ‘parallel’ Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. * checking S3 generic/method consistency ... WARNING estimate_nkr: function(x, ...) estimate_nkr.RCNA_object: function(obj, verbose) estimate_nkr: function(x, ...) estimate_nkr.default: function(df, sample.names, ano.file, out.dir, ncpus, file.ci.coverage, nkr, x.norm, norm.cov.matrix, verbose) correct_gc_bias: function(x, ...) correct_gc_bias.RCNA_object: function(obj, estimate_gc, verbose) estimate_feature_score: function(x, ...) estimate_feature_score.default: function(df, sample.names, ano.file, out.dir, ncpus, file.score.coverage, score.cutoff, low.score.cutoff, high.score.cutoff, verbose) estimate_feature_score: function(x, ...) estimate_feature_score.RCNA_object: function(obj, verbose) run_RCNA: function(x, ...) run_RCNA.default: function(sample.names, ano.file, out.dir, gcParams, win.size, gc.step, file.raw.coverage, file.corrected.coverage, file.gc.factor, estimate_gc, nkrParams, file.nkr.coverage, ncpu, nkr, x.norm, scoreParams, score.cutoff, low.score.cutoff, high.score.cutoff, commands, verbose) run_RCNA: function(x, ...) run_RCNA.RCNA_object: function(obj, estimate_gc, verbose) See section ‘Generic functions and methods’ in the ‘Writing R Extensions’ manual. Mismatches for apparent methods not registered: correct_gc_bias: function(x, ...) correct_gc_bias.default: function(df, sample.names, ano.file, out.dir, ncpus, file.raw.coverage, file.corrected.coverage, file.gc.factor, win.size, gc.step, estimate_gc, verbose) Apparent methods for exported generics not registered: correct_gc_bias.default See section ‘Registering S3 methods’ in the ‘Writing R Extensions’ manual. * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [5s/5s] NOTE Warning: : ... may be used in an incorrect context: create_RCNA_object(sample.names = sample.names, ano.file = ano.file, ncpu = ncpus, ...) Warning: : ... may be used in an incorrect context: create_RCNA_object(sample.names = sample.names, ano.file = ano.file, ncpu = ncpus, gcParams = df, ...) Warning: : ... may be used in an incorrect context: create_RCNA_object(sample.names = sample.names, ano.file = ano.file, ncpu = ncpus, ...) Warning: : ... may be used in an incorrect context: create_RCNA_object(sample.names = sample.names, ano.file = ano.file, ncpu = ncpus, scoreParams = df, ...) Warning: : ... may be used in an incorrect context: create_RCNA_object(sample.names = sample.names, ano.file = ano.file, ncpu = ncpus, ...) Warning: : ... may be used in an incorrect context: create_RCNA_object(sample.names = sample.names, ano.file = ano.file, ncpu = ncpus, nkrParams = df, ...) correct_gc_bias.RCNA_object: no visible binding for global variable ‘x’ correct_gc_bias.default: ... may be used in an incorrect context: create_RCNA_object(sample.names = sample.names, ano.file = ano.file, ncpu = ncpus, ...) correct_gc_bias.default: ... may be used in an incorrect context: create_RCNA_object(sample.names = sample.names, ano.file = ano.file, ncpu = ncpus, gcParams = df, ...) do_estimate_feature_score: no visible binding for global variable ‘k’ do_estimate_feature_score: no visible binding for global variable ‘res’ do_estimate_nkr: no visible binding for global variable ‘k’ estimate_feature_score.default: ... may be used in an incorrect context: create_RCNA_object(sample.names = sample.names, ano.file = ano.file, ncpu = ncpus, ...) estimate_feature_score.default: ... may be used in an incorrect context: create_RCNA_object(sample.names = sample.names, ano.file = ano.file, ncpu = ncpus, scoreParams = df, ...) estimate_nkr.default: ... may be used in an incorrect context: create_RCNA_object(sample.names = sample.names, ano.file = ano.file, ncpu = ncpus, ...) estimate_nkr.default: ... may be used in an incorrect context: create_RCNA_object(sample.names = sample.names, ano.file = ano.file, ncpu = ncpus, nkrParams = df, ...) Undefined global functions or variables: k res x Warning: : ... may be used in an incorrect context: create_RCNA_object(sample.names = sample.names, ano.file = ano.file, ncpu = ncpus, ...) Warning: : ... may be used in an incorrect context: create_RCNA_object(sample.names = sample.names, ano.file = ano.file, ncpu = ncpus, gcParams = df, ...) Warning: : ... may be used in an incorrect context: create_RCNA_object(sample.names = sample.names, ano.file = ano.file, ncpu = ncpus, ...) Warning: : ... may be used in an incorrect context: create_RCNA_object(sample.names = sample.names, ano.file = ano.file, ncpu = ncpus, scoreParams = df, ...) Warning: : ... may be used in an incorrect context: create_RCNA_object(sample.names = sample.names, ano.file = ano.file, ncpu = ncpus, ...) Warning: : ... may be used in an incorrect context: create_RCNA_object(sample.names = sample.names, ano.file = ano.file, ncpu = ncpus, nkrParams = df, ...) * checking Rd files ... [0s/0s] OK * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... WARNING Undocumented arguments in Rd file 'run_RCNA.default.Rd' ‘sample.names’ ‘ano.file’ ‘out.dir’ ‘gcParams’ ‘win.size’ ‘gc.step’ ‘file.raw.coverage’ ‘file.corrected.coverage’ ‘file.gc.factor’ ‘estimate_gc’ ‘nkrParams’ ‘file.nkr.coverage’ ‘ncpu’ ‘nkr’ ‘x.norm’ ‘scoreParams’ ‘score.cutoff’ ‘low.score.cutoff’ ‘high.score.cutoff’ ‘commands’ 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 installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... NONE * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [1s/1s] OK * checking PDF version of manual ... [2s/2s] OK * checking HTML version of manual ... [0s/0s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 4 WARNINGs, 3 NOTEs