############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:coMET.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings coMET_1.36.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/coMET.Rcheck’ * using R version 4.4.0 beta (2024-04-15 r86425) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 10.3.1 GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘coMET/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘coMET’ version ‘1.36.0’ * 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 ... WARNING Found the following significant warnings: Warning: replacing previous import 'utils::findMatches' by 'S4Vectors::findMatches' when loading 'coMET' See ‘/home/biocbuild/bbs-3.19-bioc/meat/coMET.Rcheck/00install.out’ for details. * checking installed package size ... NOTE installed size is 19.0Mb sub-directories of 1Mb or more: data 7.6Mb 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 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 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' pizza: no visible global function definition for 'par' pizza: no visible global function definition for 'plot.new' pizza: no visible global function definition for 'plot.window' pizza: no visible global function definition for 'polygon' pizza: no visible global function definition for 'lines' pizza: no visible global function definition for 'text' 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 lines par plot.new plot.window polygon pos_middle_exon pos_snp snp_chrom snp_pos text trackList viewTracks Consider adding importFrom("graphics", "lines", "par", "plot.new", "plot.window", "polygon", "text") importFrom("methods", "as") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * checking Rd files ... NOTE checkRd: (-1) ChIPTF_ENCODE.Rd:36: Escaped LaTeX specials: \# * 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 ... NOTE Objects in \usage without \alias in Rd file 'check.configVar.cometlist.Rd': ‘check.configVar.cometlist’ Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed comet.web 10.923 1.687 38.046 coMET-package 9.030 1.146 31.638 HistoneAll_UCSC 6.239 0.084 6.339 chromatinHMMAll_UCSC 6.276 0.020 6.313 imprintedGenes_GTEx 5.245 0.191 5.451 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.R’ OK * 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: 1 WARNING, 5 NOTEs See ‘/home/biocbuild/bbs-3.19-bioc/meat/coMET.Rcheck/00check.log’ for details.