############################################################################## ############################################################################## ### ### 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_1.10.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/methylclock.Rcheck’ * using R version 4.4.0 (2024-04-24) * 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 13.6.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘methylclock/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘methylclock’ version ‘1.10.0’ * 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 15.0.0 (clang-1500.0.40.1)’ * used SDK: ‘MacOSX11.3.sdk’ * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF. * 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 ... 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 65.823 2.288 82.121 DNAmAge 64.632 2.342 76.377 plotDNAmAge 58.024 1.838 69.468 load_DNAmGA_Clocks_data 52.328 1.445 62.464 load_DNAm_Clocks_data 51.017 1.430 61.117 checkClocks 47.291 2.182 58.716 DNAmGA 28.837 0.938 35.607 checkClocksGA 24.795 0.888 30.703 meffilEstimateCellCountsFromBetas 18.655 0.374 20.956 getCellTypeReference 9.553 2.241 12.655 meffilListCellTypeReferences 11.188 0.178 12.495 * 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: 4 NOTEs See ‘/Users/biocbuild/bbs-3.19-bioc/meat/methylclock.Rcheck/00check.log’ for details.