##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:biodbMirbase.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --timings biodbMirbase_1.5.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/biodbMirbase.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘biodbMirbase/DESCRIPTION’ ... OK
* this is package ‘biodbMirbase’ version ‘1.5.1’
* 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’
 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/download/CURRENT/mature.fa'
  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$downloadFile(url = url, dest.file = self$getDownloadPath())
   8.             └─utils::download.file(...)
  
  [ FAIL 6 | WARN 6 | SKIP 0 | PASS 40 ]
  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/download/CURRENT/mature.fa'

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/download/CURRENT/mature.fa'
--- 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: 2 ERRORs, 1 WARNING
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/biodbMirbase.Rcheck/00check.log’
for details.

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL biodbMirbase
###
##############################################################################
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* installing to library ‘/home/biocbuild/R/R-4.3.1/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: aarch64-unknown-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")
trying URL 'https://www.mirbase.org/download/CURRENT/mature.fa'
trying URL 'https://www.mirbase.org/download/CURRENT/mature.fa'
trying URL 'https://www.mirbase.org/download/CURRENT/mature.fa'
trying URL 'https://www.mirbase.org/download/CURRENT/mature.fa'
trying URL 'https://www.mirbase.org/download/CURRENT/mature.fa'
trying URL 'https://www.mirbase.org/download/CURRENT/mature.fa'
[ FAIL 6 | WARN 6 | SKIP 0 | PASS 40 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error (???): RT unit is defined when there is an RT value. ──────────────────
Error in `utils::download.file(url = url, destfile = dest.file, mode = "wb", 
    method = "auto", cacheOK = FALSE, quiet = FALSE)`: cannot open URL 'https://www.mirbase.org/download/CURRENT/mature.fa'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<MrbsMtrC>`, opt = `<named list>`)
 3.   └─conn$getBiodb()$getFactory()$getEntry(...)
 4.     └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
 5.       └─conn$getEntryContent(ids)
 6.         └─self$download()
 7.           └─private$doDownload()
 8.             └─sched$downloadFile(url = url, dest.file = self$getDownloadPath())
 9.               └─utils::download.file(...)
── Error (???): We can load an entry from the database. ────────────────────────
Error in `utils::download.file(url = url, destfile = dest.file, mode = "wb", 
    method = "auto", cacheOK = FALSE, quiet = FALSE)`: cannot open URL 'https://www.mirbase.org/download/CURRENT/mature.fa'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<MrbsMtrC>`, opt = `<named list>`)
  3.   └─opt$refEntries$getRealEntry(id)
  4.     └─self$getRealEntries(ids = id)
  5.       └─private$bdb$getFactory()$getEntry(...)
  6.         └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  7.           └─conn$getEntryContent(ids)
  8.             └─self$download()
  9.               └─private$doDownload()
 10.                 └─sched$downloadFile(url = url, dest.file = self$getDownloadPath())
 11.                   └─utils::download.file(...)
── Error (???): Wrong entry gives NULL ─────────────────────────────────────────
Error in `utils::download.file(url = url, destfile = dest.file, mode = "wb", 
    method = "auto", cacheOK = FALSE, quiet = FALSE)`: cannot open URL 'https://www.mirbase.org/download/CURRENT/mature.fa'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<MrbsMtrC>`)
 3.   └─biodb$getFactory()$getEntry(db.name, id = "WRONGA")
 4.     └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
 5.       └─conn$getEntryContent(ids)
 6.         └─self$download()
 7.           └─private$doDownload()
 8.             └─sched$downloadFile(url = url, dest.file = self$getDownloadPath())
 9.               └─utils::download.file(...)
── Error (???): One wrong entry does not block the retrieval of good ones ──────
Error in `utils::download.file(url = url, destfile = dest.file, mode = "wb", 
    method = "auto", cacheOK = FALSE, quiet = FALSE)`: cannot open URL 'https://www.mirbase.org/download/CURRENT/mature.fa'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<MrbsMtrC>`, opt = `<named list>`)
 3.   └─biodb$getFactory()$getEntry(db.name, id = ids)
 4.     └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
 5.       └─conn$getEntryContent(ids)
 6.         └─self$download()
 7.           └─private$doDownload()
 8.             └─sched$downloadFile(url = url, dest.file = self$getDownloadPath())
 9.               └─utils::download.file(...)
── Error (???): The peak table is correct. ─────────────────────────────────────
Error in `utils::download.file(url = url, destfile = dest.file, mode = "wb", 
    method = "auto", cacheOK = FALSE, quiet = FALSE)`: cannot open URL 'https://www.mirbase.org/download/CURRENT/mature.fa'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<MrbsMtrC>`, opt = `<named list>`)
 3.   └─biodb$getFactory()$getEntry(...)
 4.     └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
 5.       └─conn$getEntryContent(ids)
 6.         └─self$download()
 7.           └─private$doDownload()
 8.             └─sched$downloadFile(url = url, dest.file = self$getDownloadPath())
 9.               └─utils::download.file(...)
── Error (???): We can get a list of entry ids. ────────────────────────────────
Error in `utils::download.file(url = url, destfile = dest.file, mode = "wb", 
    method = "auto", cacheOK = FALSE, quiet = FALSE)`: cannot open URL 'https://www.mirbase.org/download/CURRENT/mature.fa'
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$downloadFile(url = url, dest.file = self$getDownloadPath())
 8.             └─utils::download.file(...)

[ FAIL 6 | WARN 6 | SKIP 0 | PASS 40 ]
Error: Test failures
Execution halted