############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:AnnotationDbi.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings AnnotationDbi_1.69.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/AnnotationDbi.Rcheck’ * using R Under development (unstable) (2024-11-24 r87369) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (conda-forge gcc 14.2.0-1) 14.2.0 GNU Fortran (conda-forge gcc 14.2.0-1) 14.2.0 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘AnnotationDbi/DESCRIPTION’ ... OK * this is package ‘AnnotationDbi’ version ‘1.69.0’ * 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 ‘AnnotationDbi’ can be installed ... OK * checking installed package size ... INFO installed size is 8.3Mb sub-directories of 1Mb or more: R 1.0Mb extdata 6.0Mb * 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 ... 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 ... NOTE Unexported object imported by a ':::' call: ‘BiocGenerics:::testPackage’ See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE createORGANISMSeeds: no visible global function definition for ‘makeAnnDbMapSeeds’ Undefined global functions or variables: makeAnnDbMapSeeds * checking Rd files ... WARNING checkRd: (5) AnnDbObj-class.Rd:58-61: \item in \describe must have non-empty label checkRd: (5) AnnDbObj-class.Rd:64-68: \item in \describe must have non-empty label checkRd: (5) AnnDbObj-class.Rd:71-75: \item in \describe must have non-empty label checkRd: (5) AnnDbObj-class.Rd:78-89: \item in \describe must have non-empty label checkRd: (5) AnnDbObj-class.Rd:92-96: \item in \describe must have non-empty label checkRd: (5) Bimap.Rd:79-82: \item in \describe must have non-empty label checkRd: (5) Bimap.Rd:84-87: \item in \describe must have non-empty label checkRd: (-1) inpIDMapper.Rd:91: Escaped LaTeX specials: \# checkRd: (-1) inpIDMapper.Rd:95: Escaped LaTeX specials: \# checkRd: (-1) inpIDMapper.Rd:99: 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 ... 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 AnnDbPkg-checker 53.075 1.098 56.051 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘AnnotationDbi_unit_tests.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, 2 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/AnnotationDbi.Rcheck/00check.log’ for details.