############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:chipenrich.data.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings chipenrich.data_2.20.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.15-data-experiment/meat/chipenrich.data.Rcheck’ * using R version 4.2.1 (2022-06-23) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘chipenrich.data/DESCRIPTION’ ... OK * this is package ‘chipenrich.data’ version ‘2.20.0’ * 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 ‘chipenrich.data’ can be installed ... WARNING Found the following significant warnings: Warning: objects ‘gene.enh.desc’, ‘gene.enh.desc’ are created by more than one data call See ‘/home/biocbuild/bbs-3.15-data-experiment/meat/chipenrich.data.Rcheck/00install.out’ for details. * checking installed package size ... NOTE installed size is 228.4Mb sub-directories of 1Mb or more: data 227.7Mb * 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 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 ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Undocumented code objects: ‘enhancer.hg19’ ‘enhancer.hg38’ ‘gene.enh.desc.hg19’ ‘geneset.cellType.hsa’ ‘locusdef.hg19.enhancer’ ‘locusdef.hg19.enhancer_plus5kb’ ‘locusdef.hg38.enhancer’ ‘locusdef.hg38.enhancer_plus5kb’ ‘mm10’ ‘mm9’ Undocumented data sets: ‘enhancer.hg19’ ‘enhancer.hg38’ ‘mm10’ ‘mm9’ ‘gene.enh.desc.hg19’ ‘geneset.cellType.hsa’ ‘locusdef.hg19.enhancer’ ‘locusdef.hg19.enhancer_plus5kb’ ‘locusdef.hg38.enhancer’ ‘locusdef.hg38.enhancer_plus5kb’ All user-level objects in a package should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * 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 LazyData ... WARNING LazyData DB of 230.8 MB without LazyDataCompression set See §1.1.6 of 'Writing R Extensions' * checking data for ASCII and uncompressed saves ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... 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 WARNINGs, 1 NOTE See ‘/home/biocbuild/bbs-3.15-data-experiment/meat/chipenrich.data.Rcheck/00check.log’ for details.