############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:methylclock.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings methylclock_1.13.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/methylclock.Rcheck’ * using R Under development (unstable) (2025-02-19 r87757) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘methylclock/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘methylclock’ version ‘1.13.0’ * 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: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’ * 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 loading without being on the library search path ... 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 54.362 2.406 106.666 plotDNAmAge 46.206 3.289 84.588 DNAmAge 41.740 2.508 78.352 checkClocks 39.409 1.974 75.470 load_DNAm_Clocks_data 38.975 2.401 70.091 load_DNAmGA_Clocks_data 35.224 2.253 70.023 DNAmGA 23.621 1.090 45.296 checkClocksGA 23.252 1.038 45.023 meffilEstimateCellCountsFromBetas 11.562 0.666 18.815 getCellTypeReference 6.673 0.736 12.190 meffilListCellTypeReferences 5.908 0.239 9.677 * 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 ‘/home/biocbuild/bbs-3.21-bioc/meat/methylclock.Rcheck/00check.log’ for details.