############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:ELMER.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings ELMER_2.31.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/ELMER.Rcheck’ * using R Under development (unstable) (2025-01-20 r87609) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘ELMER/DESCRIPTION’ ... OK * this is package ‘ELMER’ version ‘2.31.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 38 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use conditionally. * 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 ‘ELMER’ can be installed ... OK * 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 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE addMutCol: no visible binding for global variable 'Hugo_Symbol' calcDistNearestTSS: no visible binding for global variable 'DistanceTSS' getRegionNearGenes : f: no visible binding for global variable 'Side' getRegionNearGenes: no visible binding for global variable 'ID' getTFtargets: no visible binding for global variable 'TF' Undefined global functions or variables: DistanceTSS Hugo_Symbol ID Side TF * checking Rd files ... NOTE checkRd: (-1) createBigWigDNAmetArray.Rd:22: Lost braces; missing escapes or markup? 22 | \item{track.names}{Provide a list of track names (.bw) otherwise the deault is the will be {samples}.bw} | ^ * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed TCGA.pipe 68.979 2.385 72.751 getRandomPairs 36.443 2.739 43.734 get.enriched.motif 28.586 3.036 50.072 schematic.plot 22.432 1.548 32.567 createMAE 21.637 2.014 24.451 get.feature.probe 12.904 2.896 29.406 scatter.plot 13.904 0.697 14.618 get.pair 10.709 0.539 12.347 GetNearGenes 8.723 0.202 8.928 preAssociationProbeFiltering 7.700 0.836 8.768 getRegionNearGenes 6.286 0.091 6.379 get.permu 5.844 0.077 7.596 getTCGA 2.826 0.404 8.115 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/ELMER.Rcheck/00check.log’ for details.