############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:RLSeq.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings RLSeq_1.9.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/RLSeq.Rcheck’ * using R Under development (unstable) (2024-01-16 r85808) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.3 LTS * using session charset: UTF-8 * checking for file ‘RLSeq/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘RLSeq’ version ‘1.9.0’ * 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 ‘RLSeq’ 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 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 whether startup messages can be suppressed ... 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 ... 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed report 55.716 3.780 60.623 RLSeq 32.573 1.272 36.164 predictCondition 15.409 0.400 16.357 plotEnrichment 13.672 0.296 14.180 txFeatureOverlap 10.736 0.492 11.354 plotRLRegionOverlap 9.350 0.655 10.805 geneAnnotation 8.764 0.496 9.840 featureEnrich 8.744 0.221 9.147 corrHeatmap 6.926 0.652 7.667 plotTxFeatureOverlap 5.983 0.504 6.880 RLRangesFromRLBase 3.986 0.233 5.422 * 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: OK