############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:methylclock.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings methylclock_1.5.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/methylclock.Rcheck’ * using R Under development (unstable) (2023-02-14 r83833) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0 GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0 * running under: Ubuntu 20.04.6 LTS * using session charset: UTF-8 * checking for file ‘methylclock/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘methylclock’ version ‘1.5.0’ * 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: ‘g++ (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0’ * 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 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 40.120 0.960 46.869 DNAmAge 37.379 1.183 42.333 plotDNAmAge 28.857 0.903 33.598 checkClocks 26.514 0.825 31.341 load_DNAmGA_Clocks_data 24.874 0.759 29.075 load_DNAm_Clocks_data 22.575 0.649 26.579 DNAmGA 18.420 0.456 21.185 checkClocksGA 15.128 0.380 17.568 meffilEstimateCellCountsFromBetas 7.525 0.152 8.442 meffilListCellTypeReferences 6.664 0.131 7.082 getCellTypeReference 5.847 0.624 6.757 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘methylclock.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... ERROR Error(s) in re-building vignettes: ... --- re-building ‘methylclock.Rmd’ using rmarkdown The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/methylclock.Rcheck/vign_test/methylclock/vignettes/methylclock_files/figure-html/horvat_age-1.png" but not available. The magick package is required to crop "/home/biocbuild/bbs-3.17-bioc/meat/methylclock.Rcheck/vign_test/methylclock/vignettes/methylclock_files/figure-html/bnn_age-1.png" but not available. Quitting from lines 531-540 (methylclock.Rmd) Error: processing vignette 'methylclock.Rmd' failed with diagnostics: HTTP error 404. --- failed re-building ‘methylclock.Rmd’ SUMMARY: processing the following file failed: ‘methylclock.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 3 NOTEs See ‘/home/biocbuild/bbs-3.17-bioc/meat/methylclock.Rcheck/00check.log’ for details.