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### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD check --install=check:ENCODExplorerData.install-out.txt --library=/home/biocbuild/bbs-3.24-bioc/R/site-library --timings ENCODExplorerData_0.99.5.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.24-data-annotation/meat/ENCODExplorerData.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-05-20 10:06:45 UTC
* checking for file ‘ENCODExplorerData/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ENCODExplorerData’ version ‘0.99.5’
* 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 ‘ENCODExplorerData’ 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 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 ... OK
* 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 ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  encode_df_full.Rd: data.table
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘ENCODExplorerData-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: encode_df_full
> ### Title: ENCODE file metadata, Full version
> ### Aliases: encode_df_full
> 
> ### ** Examples
> 
>     # You can use AnnotationHub to retrieve encode_df_full.
>     library(AnnotationHub)
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: ‘generics’

The following objects are masked from ‘package:base’:

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


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, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: BiocFileCache
Loading required package: dbplyr
>     hub <- AnnotationHub()
>     myfiles <- subset(hub, title=="ENCODE File Metadata (Full, 2019-04-12 build)")
> 
>     # You can then have a look at the metadata of the retrieved object.
>     myfiles
AnnotationHub with 1 record
# snapshotDate(): 2026-05-19
# names(): AH69291
# $dataprovider: ENCODE Project
# $species: NA
# $rdataclass: data.table
# $rdatadateadded: 2019-04-18
# $title: ENCODE File Metadata (Full, 2019-04-12 build)
# $description: A data-frame containing a large selection of metadata descri...
# $taxonomyid: NA
# $genome: NA
# $sourcetype: JSON
# $sourceurl: https://www.encodeproject.org/
# $sourcesize: NA
# $tags: c("ENCODE", "ENCODExplorerData") 
# retrieve record with 'object[["AH69291"]]' 
> 
>     # Finally, you can access the data.table itself by indexing into the 
>     # object returned by subset.
>     myfiles[[1]]
downloading 1 resources
retrieving 1 resource
Warning: download failed
  web resource path: ‘https://annotationhub.bioconductor.org/fetch/76037’
  local file path: ‘/home/biocbuild/.cache/R/AnnotationHub/2e82722f00552f_76037’
  reason: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_disk()`:
! Timeout was reached [mghp.osn.xsede.org]:
SSL connection timeout
Warning: bfcadd() failed; resource removed
  rid: BFC236
  fpath: ‘https://annotationhub.bioconductor.org/fetch/76037’
  reason: download failed
Warning: download failed
  hub path: ‘https://annotationhub.bioconductor.org/fetch/76037’
  cache resource: ‘AH69291 : 76037’
  reason: bfcadd() failed; see warnings()
Error loading resource.
 attempting to re-download
downloading 1 resources
retrieving 1 resource
Warning: download failed
  web resource path: ‘https://annotationhub.bioconductor.org/fetch/76037’
  local file path: ‘/home/biocbuild/.cache/R/AnnotationHub/2e8272d8004eb_76037’
  reason: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_disk()`:
! Timeout was reached [mghp.osn.xsede.org]:
SSL connection timeout
Warning: bfcadd() failed; resource removed
  rid: BFC237
  fpath: ‘https://annotationhub.bioconductor.org/fetch/76037’
  reason: download failed
Warning: download failed
  hub path: ‘https://annotationhub.bioconductor.org/fetch/76037’
  cache resource: ‘AH69291 : 76037’
  reason: bfcadd() failed; see warnings()
Error: failed to load resource
  name: AH69291
  title: ENCODE File Metadata (Full, 2019-04-12 build)
  reason: 1 resources failed to download
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.24-data-annotation/meat/ENCODExplorerData.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD INSTALL ENCODExplorerData
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.24-bioc/R/site-library’
* installing *source* package ‘ENCODExplorerData’ ...
** this is package ‘ENCODExplorerData’ version ‘0.99.5’
** 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 (ENCODExplorerData)

R version 4.6.0 RC (2026-04-17 r89917) -- "Because it was There"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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.

> #Run all tests in the ENCODExplorer package
> BiocGenerics:::testPackage("ENCODExplorerData")


RUNIT TEST PROTOCOL -- Wed May 20 06:07:49 2026 
*********************************************** 
Number of test functions: 9 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
ENCODExplorerData RUnit Tests - 9 test functions, 0 errors, 0 failures
Number of test functions: 9 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  0.727   0.082   0.796