############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CSSP.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CSSP_1.30.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/CSSP.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘CSSP/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘CSSP’ version ‘1.30.0’ * 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 ... NOTE Found the following hidden files and directories: .git_fetch_output.txt .git_merge_output.txt These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘CSSP’ 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 ... NOTE Namespaces in Imports field not imported from: ‘methods’ ‘stats’ ‘utils’ All declared Imports should be used. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .allFit: no visible global function definition for ‘quantile’ .allFit: no visible global function definition for ‘model.matrix’ .allFit: no visible global function definition for ‘glm’ .csspfit : pval.nb.cont.trunc: no visible global function definition for ‘runif’ .csspfit : pval.nb.cont.trunc: no visible global function definition for ‘pnbinom’ .csspfit : pval.nb.cont: no visible global function definition for ‘runif’ .csspfit : pval.nb.cont: no visible global function definition for ‘pnbinom’ .csspfit : pval.mod.w: no visible global function definition for ‘dnbinom’ .csspfit: no visible global function definition for ‘pnbinom’ .csspfit: no visible global function definition for ‘dnbinom’ .csspfit: no visible global function definition for ‘weighted.mean’ .csspfit: no visible global function definition for ‘na.omit’ .csspfit: no visible global function definition for ‘new’ .gridFit: no visible global function definition for ‘quantile’ .gridFit: no visible global function definition for ‘model.matrix’ .gridFit: no visible global function definition for ‘glm’ .gridFit: no visible global function definition for ‘predict.glm’ .nonpaFit: no visible global function definition for ‘quantile’ .nonpaFit: no visible global function definition for ‘weighted.mean’ createBinData: no visible global function definition for ‘read.table’ createBinData: no visible global function definition for ‘new’ createBinData: no visible global function definition for ‘na.omit’ readBinFile: no visible global function definition for ‘read.table’ callpeak,CSSPFit: no visible global function definition for ‘pnbinom’ callpeak,CSSPFit: no visible global function definition for ‘pgamma’ cssp.power,CSSPFit: no visible global function definition for ‘rgamma’ cssp.power,CSSPFit: no visible global function definition for ‘rbinom’ cssp.power,CSSPFit: no visible global function definition for ‘rpois’ cssp.power,CSSPFit: no visible global function definition for ‘pnbinom’ cssp.power,CSSPFit: no visible global function definition for ‘na.omit’ cssp.power,CSSPFit: no visible global function definition for ‘pgamma’ cssp.power,CSSPFit: no visible global function definition for ‘qnbinom’ cssp.power,CSSPFit: no visible global function definition for ‘qgamma’ cssp.power,CSSPFit: no visible global function definition for ‘runif’ cssp.power,CSSPFit: no visible global function definition for ‘weighted.mean’ cssp.sim,CSSPFit: no visible global function definition for ‘rgamma’ cssp.sim,CSSPFit: no visible global function definition for ‘rbinom’ cssp.sim,CSSPFit: no visible global function definition for ‘runif’ fit.freq,CSSPFit: no visible global function definition for ‘quantile’ fit.freq,CSSPFit : : no visible global function definition for ‘dnbinom’ pBBT,CSSPFit: no visible global function definition for ‘pgamma’ qBBT,CSSPFit: no visible global function definition for ‘quantile’ qBBT,CSSPFit: no visible global function definition for ‘uniroot’ show,CSSPFit: no visible global function definition for ‘showClass’ Undefined global functions or variables: dnbinom glm model.matrix na.omit new pgamma pnbinom predict.glm qgamma qnbinom quantile rbinom read.table rgamma rpois runif showClass uniroot weighted.mean Consider adding importFrom("methods", "new", "showClass") importFrom("stats", "dnbinom", "glm", "model.matrix", "na.omit", "pgamma", "pnbinom", "predict.glm", "qgamma", "qnbinom", "quantile", "rbinom", "rgamma", "rpois", "runif", "uniroot", "weighted.mean") importFrom("utils", "read.table") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * 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 line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... 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 cssp.power-methods 18.548 0.455 19.019 cssp.fit-methods 6.199 0.101 6.305 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘run_tests.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: 3 NOTEs See ‘/Users/biocbuild/bbs-3.13-bioc/meat/CSSP.Rcheck/00check.log’ for details.