##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:AnnotationHub.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings AnnotationHub_3.10.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.18-bioc/meat/AnnotationHub.Rcheck'
* using R version 4.3.3 (2024-02-29 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.3.0
    GNU Fortran (GCC) 12.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'AnnotationHub/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'AnnotationHub' version '3.10.1'
* 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 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 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 37.82   1.84   41.28
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 1 NOTE
See
  'F:/biocbuild/bbs-3.18-bioc/meat/AnnotationHub.Rcheck/00check.log'
for details.