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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:biodbMirbase.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings biodbMirbase_1.4.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/biodbMirbase.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘biodbMirbase/DESCRIPTION’ ... OK
* this is package ‘biodbMirbase’ version ‘1.4.0’
* 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 ‘biodbMirbase’ can be installed ... OK
* checking installed package size ... OK
* checking package 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 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 ... 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 ... ERROR
Running examples in ‘biodbMirbase-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: MirbaseMatureConn
> ### Title: miRBase mature database connector class.
> ### Aliases: MirbaseMatureConn
> 
> ### ** Examples
> 
> # Create an instance with default settings:
> mybiodb <- biodb::newInst()
INFO  [19:59:08.830] Loading definitions from package biodb version 1.8.0.
INFO  [19:59:09.231] Loading definitions from package biodbMirbase version 1.4.0.
> 
> # Get a connector:
> conn <- mybiodb$getFactory()$createConn('mirbase.mature')
> 
> # Get the first entry
> e <- conn$getEntry('MIMAT0000433')
INFO  [19:59:09.345] Create cache folder "/home/biocbuild/.cache/R/biodb/mirbase.mature-ecbae556d51779d9d48125ba5a617e19" for "mirbase.mature-ecbae556d51779d9d48125ba5a617e19".
INFO  [19:59:09.347] Downloading whole database of mirbase.mature.
trying URL 'https://www.mirbase.org/ftp/CURRENT/mature.fa.gz'
Warning in utils::download.file(url = url, destfile = dest.file, mode = "wb",  :
  downloaded length 0 != reported length 0
Warning in utils::download.file(url = url, destfile = dest.file, mode = "wb",  :
  cannot open URL 'https://www.mirbase.org/ftp/CURRENT/mature.fa.gz': HTTP status was '404 Not Found'
Error in utils::download.file(url = url, destfile = dest.file, mode = "wb",  : 
  cannot open URL 'https://www.mirbase.org/ftp/CURRENT/mature.fa.gz'
Calls: <Anonymous> ... <Anonymous> -> <Anonymous> -> <Anonymous> -> <Anonymous>
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
      method = "auto", cacheOK = FALSE, quiet = FALSE)`: cannot open URL 'https://www.mirbase.org/ftp/CURRENT/mature.fa.gz'
  Backtrace:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<MrbsMtrC>`)
   3.   └─conn$getEntryIds(max.results = max)
   4.     └─private$doGetEntryIds(max.results = max.results, ...)
   5.       └─self$download()
   6.         └─private$doDownload()
   7.           └─sched$downloadFile(url = gz.url, dest.file = self$getDownloadPath())
   8.             └─utils::download.file(...)
  
  [ FAIL 8 | WARN 12 | SKIP 0 | PASS 41 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘biodbMirbase.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘biodbMirbase.Rmd’ using rmarkdown
trying URL 'https://www.mirbase.org/ftp/CURRENT/mature.fa.gz'

Quitting from lines 65-67 [unnamed-chunk-4] (biodbMirbase.Rmd)
Error: processing vignette 'biodbMirbase.Rmd' failed with diagnostics:
cannot open URL 'https://www.mirbase.org/ftp/CURRENT/mature.fa.gz'
--- failed re-building ‘biodbMirbase.Rmd’

SUMMARY: processing the following file failed:
  ‘biodbMirbase.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 3 ERRORs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/biodbMirbase.Rcheck/00check.log’
for details.