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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:AnnotationHub.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings AnnotationHub_3.7.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/AnnotationHub.Rcheck’
* using R Under development (unstable) (2023-01-10 r83596)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* R was compiled by
    Apple clang version 12.0.0 (clang-1200.0.32.29)
    GNU Fortran (GCC) 8.2.0
* running under: macOS Mojave 10.14.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AnnotationHub/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AnnotationHub’ version ‘3.7.0’
* 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 dependencies in R code ... WARNING
'::' or ':::' imports not declared from:
  ‘CompoundDb’ ‘ensembldb’
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:134-142: \item in \describe must have non-empty label
checkRd: (5) AnnotationHub-class.Rd:151-154: \item in \describe must have non-empty label
checkRd: (5) AnnotationHub-class.Rd:155-158: \item in \describe must have non-empty label
checkRd: (5) AnnotationHub-class.Rd:159-162: \item in \describe must have non-empty label
checkRd: (5) AnnotationHub-class.Rd:163-166: \item in \describe must have non-empty label
checkRd: (5) AnnotationHub-class.Rd:167-171: \item in \describe must have non-empty label
checkRd: (5) AnnotationHub-class.Rd:172-178: \item in \describe must have non-empty label
checkRd: (5) AnnotationHub-class.Rd:179-213: \item in \describe must have non-empty label
checkRd: (5) AnnotationHub-class.Rd:215-217: \item in \describe must have non-empty label
checkRd: (5) AnnotationHub-class.Rd:219-221: \item in \describe must have non-empty label
checkRd: (5) AnnotationHub-class.Rd:223-225: \item in \describe must have non-empty label
checkRd: (5) AnnotationHub-class.Rd:234-238: \item in \describe must have non-empty label
checkRd: (5) AnnotationHub-class.Rd:239-243: \item in \describe must have non-empty label
checkRd: (5) AnnotationHub-class.Rd:244-250: \item in \describe must have non-empty label
checkRd: (5) AnnotationHub-class.Rd:251-272: \item in \describe must have non-empty label
checkRd: (5) AnnotationHub-class.Rd:273-281: \item in \describe must have non-empty label
checkRd: (5) AnnotationHub-class.Rd:282-287: \item in \describe must have non-empty label
checkRd: (5) AnnotationHub-class.Rd:288-293: \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:305-309: \item in \describe must have non-empty label
checkRd: (5) AnnotationHub-class.Rd:310-321: \item in \describe must have non-empty label
checkRd: (5) AnnotationHub-class.Rd:322-325: \item in \describe must have non-empty label
checkRd: (5) AnnotationHub-class.Rd:326-329: \item in \describe must have non-empty label
checkRd: (5) AnnotationHub-class.Rd:330-337: \item in \describe must have non-empty label
checkRd: (5) AnnotationHub-class.Rd:338-345: \item in \describe must have non-empty label
checkRd: (5) AnnotationHub-class.Rd:346-351: \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-class.Rd:363-367: \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 ... 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
AnnotationHub-class 71.685  1.869 110.712
* 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
See
  ‘/Users/biocbuild/bbs-3.17-bioc/meat/AnnotationHub.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL AnnotationHub
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3/Resources/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 Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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

snapshotDate(): 2022-12-16
Using 'localHub=TRUE'
  If offline, please also see BiocManager vignette section on offline use
snapshotDate(): 2022-12-16
snapshotDate(): 2022-12-16
snapshotDate(): 2022-12-16
snapshotDate(): 2022-12-16
snapshotDate(): 2022-12-16
snapshotDate(): 2022-12-16
snapshotDate(): 2022-12-16
snapshotDate(): 2022-12-16
snapshotDate(): 2022-12-16
snapshotDate(): 2022-12-16
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    I, expand.grid, unname

require("xxx_foo")


RUNIT TEST PROTOCOL -- Sun Feb  5 22:27:53 2023 
*********************************************** 
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 
 84.098   8.034 124.723