############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:cqn.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings cqn_1.48.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/cqn.Rcheck’ * using R version 4.3.2 Patched (2023-11-01 r85457) * using platform: x86_64-apple-darwin20 (64-bit) * R was compiled by Apple clang version 14.0.3 (clang-1403.0.22.14.1) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘cqn/DESCRIPTION’ ... OK * this is package ‘cqn’ version ‘1.48.0’ * 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 ‘cqn’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Package listed in more than one of Depends, Imports, Suggests, Enhances: ‘splines’ A package should be listed in only one of these fields. * 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 ... NOTE Packages in Depends field not imported from: ‘mclust’ ‘preprocessCore’ ‘quantreg’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE SQN2: no visible binding for global variable ‘median’ SQN2: no visible global function definition for ‘Mclust’ cqn : fixPredictor: no visible global function definition for ‘quantile’ cqn: no visible global function definition for ‘median’ cqn : : no visible global function definition for ‘rq’ cqn : : no visible global function definition for ‘predict’ cqn : : no visible global function definition for ‘coef’ cqnplot: no visible global function definition for ‘matplot’ cqnplot: no visible global function definition for ‘rug’ mix.qn: no visible global function definition for ‘ecdf’ mix.qn: no visible global function definition for ‘quantile’ norm.pickrell: no visible global function definition for ‘quantile’ norm.pickrell : : no visible global function definition for ‘smooth.spline’ norm.pickrell : : no visible global function definition for ‘predict’ Undefined global functions or variables: Mclust coef ecdf matplot median predict quantile rq rug smooth.spline Consider adding importFrom("graphics", "matplot", "rug") importFrom("stats", "coef", "ecdf", "median", "predict", "quantile", "smooth.spline") 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... 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: 3 NOTEs See ‘/Users/biocbuild/bbs-3.18-bioc/meat/cqn.Rcheck/00check.log’ for details.