############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:methylMnM.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings methylMnM_1.30.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/methylMnM.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 ‘methylMnM/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘methylMnM’ 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 ‘methylMnM’ can be installed ... OK * checking installed package size ... NOTE installed size is 47.6Mb sub-directories of 1Mb or more: extdata 47.4Mb * 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 'library' or 'require' calls to packages already attached by Depends: ‘edgeR’ ‘statmod’ Please remove these calls from your code. Packages in Depends field not imported from: ‘edgeR’ ‘statmod’ 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 CNVnormal: no visible global function definition for ‘read.table’ MnM.qvalue: no visible global function definition for ‘read.table’ MnM.qvalue: no visible global function definition for ‘write.table’ MnM.selectDMR: no visible global function definition for ‘quantile’ MnM.test: no visible global function definition for ‘read.table’ MnM.test: no visible global function definition for ‘calcNormFactors’ MnM.test: no visible global function definition for ‘sage.test’ MnM.test: no visible global function definition for ‘lm’ MnM.test: no visible global function definition for ‘write.table’ countMREbin: no visible global function definition for ‘read.table’ countMREbin: no visible global function definition for ‘count.fields’ countMREbin: no visible global function definition for ‘write.table’ countMREcpgbin: no visible global function definition for ‘read.table’ countMREcpgbin: no visible global function definition for ‘count.fields’ countMREcpgbin: no visible global function definition for ‘write.table’ countMeDIPbin: no visible global function definition for ‘read.table’ countMeDIPbin: no visible global function definition for ‘count.fields’ countMeDIPbin: no visible global function definition for ‘write.table’ countcpgbin: no visible global function definition for ‘read.table’ countcpgbin: no visible global function definition for ‘count.fields’ countcpgbin: no visible global function definition for ‘write.table’ normpdf: no visible global function definition for ‘pnorm’ removeblacklist: no visible global function definition for ‘read.table’ Undefined global functions or variables: calcNormFactors count.fields lm pnorm quantile read.table sage.test write.table Consider adding importFrom("stats", "lm", "pnorm", "quantile") importFrom("utils", "count.fields", "read.table", "write.table") 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 line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available File ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/methylMnM/libs/methylMnM.so’: Found ‘_printf’, possibly from ‘printf’ (C) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs. The detected symbols are linked into the code but might come from libraries and not actually be called. See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. * 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: 5 NOTEs See ‘/Users/biocbuild/bbs-3.13-bioc/meat/methylMnM.Rcheck/00check.log’ for details.