############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:snm.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings snm_1.54.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/snm.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.6.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘snm/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘snm’ version ‘1.54.0’ * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 ‘snm’ 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 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 buildBasisSplineMatrix : : no visible global function definition for ‘predict’ calcArrayEffects : : no visible global function definition for ‘predict’ edge.glr: no visible global function definition for ‘pf’ edge.qvalue: no visible global function definition for ‘smooth.spline’ edge.qvalue: no visible global function definition for ‘predict’ fit.model: no visible binding for global variable ‘weighted.mean’ fit.model: no visible global function definition for ‘residuals’ getSpanningSet: no visible global function definition for ‘quantile’ make.ref.model.matrices: no visible global function definition for ‘model.matrix’ make.ref.model.matrices: no visible global function definition for ‘as.formula’ make.snm.obj: no visible global function definition for ‘model.matrix’ sim.doubleChannel: no visible global function definition for ‘rchisq’ sim.doubleChannel: no visible global function definition for ‘runif’ sim.doubleChannel: no visible global function definition for ‘rnorm’ sim.doubleChannel: no visible binding for global variable ‘rnorm’ sim.doubleChannel: no visible global function definition for ‘model.matrix’ sim.function.var: no visible global function definition for ‘model.matrix’ sim.intensity.dep: no visible global function definition for ‘model.matrix’ sim.intensity.dep: no visible global function definition for ‘predict’ sim.preProcessed: no visible global function definition for ‘rchisq’ sim.preProcessed: no visible global function definition for ‘runif’ sim.preProcessed: no visible global function definition for ‘rnorm’ sim.preProcessed: no visible binding for global variable ‘rnorm’ sim.preProcessed: no visible global function definition for ‘model.matrix’ sim.probe.specific: no visible global function definition for ‘model.matrix’ sim.refDesign: no visible global function definition for ‘rchisq’ sim.refDesign: no visible global function definition for ‘runif’ sim.refDesign: no visible binding for global variable ‘rnorm’ sim.refDesign: no visible global function definition for ‘rnorm’ sim.refDesign: no visible global function definition for ‘model.matrix’ sim.singleChannel: no visible global function definition for ‘rchisq’ sim.singleChannel: no visible global function definition for ‘runif’ sim.singleChannel: no visible global function definition for ‘rnorm’ sim.singleChannel: no visible binding for global variable ‘rnorm’ sim.singleChannel: no visible global function definition for ‘model.matrix’ snm.diagnostic.plot: no visible global function definition for ‘par’ snm.diagnostic.plot: no visible global function definition for ‘axis’ snm.diagnostic.plot : : no visible global function definition for ‘points’ snm.diagnostic.plot: no visible global function definition for ‘hist’ snm.diagnostic.plot: no visible global function definition for ‘abline’ snm.diagnostic.plot: no visible global function definition for ‘mtext’ snm.diagnostic.plot: no visible global function definition for ‘title’ snm.plot: no visible global function definition for ‘model.matrix’ snm.plot: no visible global function definition for ‘rainbow’ snm.plot: no visible global function definition for ‘points’ snm.plot: no visible global function definition for ‘par’ snm.plot: no visible global function definition for ‘abline’ snm.plot: no visible global function definition for ‘fitted’ snm.plot: no visible global function definition for ‘hist’ snm.plot: no visible global function definition for ‘mtext’ snm.plot: no visible global function definition for ‘title’ Undefined global functions or variables: abline as.formula axis fitted hist model.matrix mtext par pf points predict quantile rainbow rchisq residuals rnorm runif smooth.spline title weighted.mean Consider adding importFrom("grDevices", "rainbow") importFrom("graphics", "abline", "axis", "hist", "mtext", "par", "points", "title") importFrom("stats", "as.formula", "fitted", "model.matrix", "pf", "predict", "quantile", "rchisq", "residuals", "rnorm", "runif", "smooth.spline", "weighted.mean") to your NAMESPACE file. * 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 sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed sim.refDesign 36.693 3.886 40.638 snm 32.288 3.743 36.051 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/Users/biocbuild/bbs-3.20-bioc/meat/snm.Rcheck/00check.log’ for details.