##############################################################################
##############################################################################
###
### 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_3.10.1.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 ‘3.10.1’
* 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 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 35.755  2.187   41.51
* 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
 OK
* 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.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL AnnotationHub
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’
* installing *source* package ‘AnnotationHub’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (AnnotationHub)

R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("AnnotationHub")

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Using 'localHub=TRUE'
  If offline, please also see BiocManager vignette section on offline use
require("xxx_foo")


RUNIT TEST PROTOCOL -- Mon Apr 15 20:05:28 2024 
*********************************************** 
Number of test functions: 20 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
AnnotationHub RUnit Tests - 20 test functions, 0 errors, 0 failures
Number of test functions: 20 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: call dbDisconnect() when finished working with a connection 
2: download failed
  hub path: 'bogus/url'
  cache resource: 'AHInvalid : 5012'
  reason: all(rtype == "web" | file.exists(fpath)) is not TRUE 
> 
> proc.time()
   user  system elapsed 
 39.786   2.558  57.630