############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:pandaR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings pandaR_1.31.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/pandaR.Rcheck’ * using R Under development (unstable) (2023-02-14 r83833) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0 GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0 * running under: Ubuntu 20.04.6 LTS * using session charset: UTF-8 * checking for file ‘pandaR/DESCRIPTION’ ... OK * this is package ‘pandaR’ version ‘1.31.0’ * 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 ‘pandaR’ can be installed ... OK * checking installed package size ... NOTE installed size is 9.4Mb sub-directories of 1Mb or more: data 9.0Mb * 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 ... WARNING Invalid citation information in ‘inst/CITATION’: Error in tools:::.parse_CITATION_file(file, meta$Encoding): non-ASCII input in a CITATION file without a declared encoding * 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 dependencies in R code ... OK * checking S3 generic/method consistency ... NOTE Found the following apparent S3 methods exported but not registered: summary.panda See section ‘Registering S3 methods’ in the ‘Writing R Extensions’ manual. * 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 ... NOTE S3 methods shown with full name in documentation object 'summary.panda': ‘summary.panda’ The \usage entries for S3 methods should use the \method markup and not their full name. 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 LazyData ... WARNING LazyData DB of 9.0 MB without LazyDataCompression set See §1.1.6 of 'Writing R Extensions' * 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 panda 11.021 0.262 16.152 testMotif 5.304 0.219 9.204 plotZbyTF 4.277 0.061 12.264 plotZ 1.923 0.075 5.461 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘pandaR.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 WARNINGs, 3 NOTEs See ‘/home/biocbuild/bbs-3.17-bioc/meat/pandaR.Rcheck/00check.log’ for details.