##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:RLHub.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings RLHub_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-data-experiment/meat/RLHub.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* 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 22.04.5 LTS
* using session charset: UTF-8
* checking for file ‘RLHub/DESCRIPTION’ ... OK
* this is package ‘RLHub’ version ‘1.10.0’
* package encoding: UTF-8
* 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 ‘RLHub’ 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 whether startup messages can be suppressed ... 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
Package unavailable to check Rd xrefs: ‘Boruta’
* 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 ... ERROR
Running examples in ‘RLHub-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gene_exp
> ### Title: Gene Expression
> ### Aliases: gene_exp
> 
> ### ** Examples
> 
> 
> geneExp <- gene_exp()
see ?RLHub and browseVignettes('RLHub') for documentation
loading from cache
require(“SummarizedExperiment”)
Error: failed to load resource
  name: EH6798
  title: Gene Expression
  reason: require(“SummarizedExperiment”) failed: use BiocManager::install() to install package?
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
   10.         └─ExperimentHub (local) .local(x, i, j = j, ...)
   11.           ├─methods::callNextMethod(x, i, j, ..., force = force, verbose = verbose)
   12.           │ └─base::eval(call, callEnv)
   13.           │   └─base::eval(call, callEnv)
   14.           └─AnnotationHub (local) .nextMethod(x, i, j, ..., force = force, verbose = verbose)
   15.             └─AnnotationHub (local) .local(x, i, j = j, ...)
   16.               └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose)
   17.                 └─base::tryCatch(...)
   18.                   └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   19.                     └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   20.                       └─value[[3L]](cond)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 5 ]
  Error: Test failures
  Execution halted
* 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: 2 ERRORs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.19-data-experiment/meat/RLHub.Rcheck/00check.log’
for details.