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###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:biodbMirbase.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings biodbMirbase_1.5.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-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 ‘1.5.0’
* 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 for missing documentation entries ... WARNING
Undocumented code objects:
  ‘MirbaseMatureConn’ ‘MirbaseMatureEntry’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... NONE
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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/download/CURRENT/mature.fa'
Content type 'text/html; charset=utf-8' length 4306170 bytes (4.1 MB)
==================================================
downloaded 4.1 MB


Quitting from lines 65-67 [unnamed-chunk-4] (biodbMirbase.Rmd)
Error: processing vignette 'biodbMirbase.Rmd' failed with diagnostics:
File /home/biocbuild/.cache/R/biodb/mirbase.mature-ee3c16b1e67d439324a1d7fe34666ec8/download.txt does not exists. Downloading went wrong.
--- 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: 1 ERROR, 1 WARNING
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/biodbMirbase.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL biodbMirbase
###
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* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’
* installing *source* package ‘biodbMirbase’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
No man pages found in package  ‘biodbMirbase’ 
*** 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 (biodbMirbase)

R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 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.

> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbMirbase)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbMirbase")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 56 ]
> 
> proc.time()
   user  system elapsed 
  4.761   0.206   5.004