############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:coMET.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings coMET_1.26.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/coMET.Rcheck’ * using R version 4.1.3 (2022-03-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘coMET/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘coMET’ version ‘1.26.0’ * 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 ‘coMET’ can be installed ... OK * checking installed package size ... NOTE installed size is 19.3Mb sub-directories of 1Mb or more: data 7.9Mb extdata 10.7Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... NOTE File LICENSE is not mentioned in the DESCRIPTION file. * 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE draw.plot.annotation : : no visible global function definition for 'ggplotGrob' draw.plot.annotation: no visible global function definition for 'viewTracks' draw.plot.annotation: no visible global function definition for 'trackList' eQTL: no visible binding for global variable 'chromosome_stop' eQTL: no visible binding for global variable 'chromosome_start' eQTL: no visible binding for global variable 'chromosome_name' eQTL_GTEx: no visible binding for global variable 'snp_pos' eQTL_GTEx: no visible binding for global variable 'snp_chrom' eQTL_GTEx: no visible binding for global variable 'gene_start' eQTL_GTEx: no visible binding for global variable 'gene_stop' eQTL_GTEx: no visible binding for global variable 'gene_chr' geneExpression_GTEx: no visible global function definition for 'as' metQTL: no visible binding for global variable 'chromosome_stop' metQTL: no visible binding for global variable 'chromosome_start' metQTL: no visible binding for global variable 'chromosome_name' psiQTL_GTEx: no visible binding for global variable 'pos_snp' psiQTL_GTEx: no visible binding for global variable 'chr_snp' psiQTL_GTEx: no visible binding for global variable 'pos_middle_exon' psiQTL_GTEx: no visible binding for global variable 'chr_exon' Undefined global functions or variables: as chr_exon chr_snp chromosome_name chromosome_start chromosome_stop gene_chr gene_start gene_stop ggplotGrob pos_middle_exon pos_snp snp_chrom snp_pos trackList viewTracks Consider adding importFrom("methods", "as") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * 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 sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed comet.web 15.343 0.207 39.019 coMET-package 9.433 0.135 15.082 chromatinHMMAll_UCSC 8.194 0.061 8.259 imprintedGenes_GTEx 8.077 0.040 8.126 HistoneAll_UCSC 8.067 0.014 8.083 comet 5.885 0.048 5.936 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.R’ OK * 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-3.14-bioc/meat/coMET.Rcheck/00check.log’ for details.