############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:AnnotationHub.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings AnnotationHub_3.10.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/AnnotationHub.Rcheck’ * using R version 4.3.3 (2024-02-29) * using platform: x86_64-pc-linux-gnu (64-bit) * 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 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘AnnotationHub/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘AnnotationHub’ version ‘3.10.0’ * 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 ‘AnnotationHub’ 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 ... NOTE Unexported objects imported by ':::' calls: 'BiocFileCache:::.get_tbl_rid' 'S4Vectors:::selectSome' 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 ... OK * checking Rd files ... WARNING checkRd: (5) AnnotationHub-class.Rd:135-143: \item in \describe must have non-empty label checkRd: (5) AnnotationHub-class.Rd:152-155: \item in \describe must have non-empty label checkRd: (5) AnnotationHub-class.Rd:156-159: \item in \describe must have non-empty label checkRd: (5) AnnotationHub-class.Rd:160-163: \item in \describe must have non-empty label checkRd: (5) AnnotationHub-class.Rd:164-167: \item in \describe must have non-empty label checkRd: (5) AnnotationHub-class.Rd:168-172: \item in \describe must have non-empty label checkRd: (5) AnnotationHub-class.Rd:173-179: \item in \describe must have non-empty label checkRd: (5) AnnotationHub-class.Rd:180-214: \item in \describe must have non-empty label checkRd: (5) AnnotationHub-class.Rd:216-218: \item in \describe must have non-empty label checkRd: (5) AnnotationHub-class.Rd:220-222: \item in \describe must have non-empty label checkRd: (5) AnnotationHub-class.Rd:224-226: \item in \describe must have non-empty label checkRd: (5) AnnotationHub-class.Rd:235-239: \item in \describe must have non-empty label checkRd: (5) AnnotationHub-class.Rd:240-244: \item in \describe must have non-empty label checkRd: (5) AnnotationHub-class.Rd:245-251: \item in \describe must have non-empty label checkRd: (5) AnnotationHub-class.Rd:252-273: \item in \describe must have non-empty label checkRd: (5) AnnotationHub-class.Rd:274-282: \item in \describe must have non-empty label checkRd: (5) AnnotationHub-class.Rd:283-288: \item in \describe must have non-empty label checkRd: (5) AnnotationHub-class.Rd:295-299: \item in \describe must have non-empty label checkRd: (5) AnnotationHub-class.Rd:300-304: \item in \describe must have non-empty label checkRd: (5) AnnotationHub-class.Rd:305-316: \item in \describe must have non-empty label checkRd: (5) AnnotationHub-class.Rd:317-320: \item in \describe must have non-empty label checkRd: (5) AnnotationHub-class.Rd:321-324: \item in \describe must have non-empty label checkRd: (5) AnnotationHub-class.Rd:325-332: \item in \describe must have non-empty label checkRd: (5) AnnotationHub-class.Rd:333-340: \item in \describe must have non-empty label checkRd: (5) AnnotationHub-class.Rd:341-346: \item in \describe must have non-empty label checkRd: (5) AnnotationHub-class.Rd:353-357: \item in \describe must have non-empty label checkRd: (5) AnnotationHub-class.Rd:358-362: \item in \describe must have non-empty label checkRd: (5) AnnotationHub-deprecated.Rd:28-34: \item in \describe must have non-empty label * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... WARNING Functions or methods with usage in documentation object 'AnnotationHub-deprecated' but not in code: ‘display’ * 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 AnnotationHub-class 34.694 1.407 37.453 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘AnnotationHub-HOWTO.Rmd’... OK ‘AnnotationHub.Rmd’ using ‘UTF-8’... OK ‘TroubleshootingTheCache.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 WARNINGs, 1 NOTE See ‘/home/biocbuild/bbs-3.18-bioc/meat/AnnotationHub.Rcheck/00check.log’ for details.