############################################################################## ############################################################################## ### ### Running command: ### ### /home/hpages/bbs-3.18-bioc/R/bin/R CMD check --install=check:BiocFileCache.install-out.txt --library=/home/hpages/bbs-3.18-bioc-testing/Rlibs --timings BiocFileCache_2.9.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/hpages/bbs-3.18-bioc-testing/meat/BiocFileCache.Rcheck’ * using R version 4.3.0 Patched (2023-05-23 r84466) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 12.2.0-17ubuntu1) 12.2.0 GNU Fortran (Ubuntu 12.2.0-17ubuntu1) 12.2.0 * running under: Ubuntu 23.04 * using session charset: UTF-8 * checking for file ‘BiocFileCache/DESCRIPTION’ ... OK * this is package ‘BiocFileCache’ version ‘2.9.0’ * 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 ‘BiocFileCache’ 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 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 ... NOTE .sql_clean_cache: no visible binding for global variable ‘rid’ .sql_clean_cache: no visible binding for global variable ‘access_time’ .sql_get_resource_table: no visible binding for global variable ‘rid’ .sql_get_resource_table: no visible binding for global variable ‘id’ Undefined global functions or variables: access_time id rid * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed BiocFileCache-class 3.591 0.068 9.894 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘BiocFileCache.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/home/hpages/bbs-3.18-bioc-testing/meat/BiocFileCache.Rcheck/00check.log’ for details.