############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:methylclock.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings methylclock_1.8.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/methylclock.Rcheck’ * using R version 4.3.3 (2024-02-29) * using platform: x86_64-apple-darwin20 (64-bit) * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) 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 ‘methylclock/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘methylclock’ version ‘1.8.0’ * package encoding: UTF-8 * 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 ‘methylclock’ can be installed ... OK * used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.sdk’ * 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 Namespace in Imports field not imported from: ‘planet’ All declared Imports should be used. Unexported object imported by a ':::' call: ‘minfi:::projectCellType’ See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE DNAmAge: no visible binding for global variable ‘coefHorvath’ DNAmAge: no visible binding for global variable ‘coefHannum’ DNAmAge: no visible binding for global variable ‘coefLevine’ DNAmAge: no visible binding for global variable ‘coefSkin’ DNAmAge: no visible binding for global variable ‘coefPedBE’ DNAmAge: no visible binding for global variable ‘coefWu’ DNAmAge: no visible binding for global variable ‘coefTL’ DNAmAge: no visible binding for global variable ‘coefBLUP’ DNAmAge: no visible binding for global variable ‘coefEN’ DNAmGA: no visible binding for global variable ‘coefKnightGA’ DNAmGA: no visible binding for global variable ‘coefBohlin’ DNAmGA: no visible binding for global variable ‘coefMayneGA’ DNAmGA: no visible binding for global variable ‘coefLeeGA’ DNAmGA: no visible binding for global variable ‘coefEPIC’ DNAmGA: no visible global function definition for ‘meffil.estimate.cell.counts.from.betas’ DNAmGA: no visible global function definition for ‘install.packages’ DNAmGA: no visible global function definition for ‘data’ DNAmGA: no visible binding for global variable ‘plCellCpGsThird’ checkClocks: no visible binding for global variable ‘MethylationData’ checkClocks: no visible binding for global variable ‘coefHorvath’ checkClocks: no visible binding for global variable ‘coefHannum’ checkClocks: no visible binding for global variable ‘coefLevine’ checkClocks: no visible binding for global variable ‘coefSkin’ checkClocks: no visible binding for global variable ‘coefPedBE’ checkClocks: no visible binding for global variable ‘coefWu’ checkClocks: no visible binding for global variable ‘coefTL’ checkClocks: no visible binding for global variable ‘coefBLUP’ checkClocks: no visible binding for global variable ‘coefEN’ checkClocksGA: no visible binding for global variable ‘coefKnightGA’ checkClocksGA: no visible binding for global variable ‘coefBohlin’ checkClocksGA: no visible binding for global variable ‘coefMayneGA’ checkClocksGA: no visible binding for global variable ‘coefLeeGA’ checkClocksGA: no visible binding for global variable ‘coefEPIC’ cpgs_imputation: no visible binding for global variable ‘cpgs.in’ plotCorClocks: no visible binding for global variable ‘method’ plotCorClocks: no visible binding for global variable ‘clock’ plotCorClocks: no visible binding for global variable ‘age’ plotCorClocks: no visible binding for global variable ‘..rr.label..’ plotCorClocks: no visible binding for global variable ‘..p.label..’ plotDNAmAge: no visible binding for global variable ‘..eq.label..’ plotDNAmAge: no visible binding for global variable ‘..rr.label..’ Undefined global functions or variables: ..eq.label.. ..p.label.. ..rr.label.. MethylationData age clock coefBLUP coefBohlin coefEN coefEPIC coefHannum coefHorvath coefKnightGA coefLeeGA coefLevine coefMayneGA coefPedBE coefSkin coefTL coefWu cpgs.in data install.packages meffil.estimate.cell.counts.from.betas method plCellCpGsThird Consider adding importFrom("utils", "data", "install.packages") 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 line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed commonClockCpgs 52.745 3.121 65.104 DNAmAge 43.240 3.585 49.934 plotDNAmAge 42.891 2.227 53.215 checkClocks 40.370 4.309 51.296 load_DNAm_Clocks_data 34.828 1.823 43.576 load_DNAmGA_Clocks_data 31.773 1.935 40.084 checkClocksGA 21.843 1.277 26.962 DNAmGA 21.418 1.266 24.197 getCellTypeReference 10.187 6.661 18.823 meffilEstimateCellCountsFromBetas 13.035 0.432 15.465 meffilListCellTypeReferences 8.743 0.246 8.243 * 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/methylclock.Rcheck/00check.log’ for details.