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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodbMirbase.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodbMirbase_1.4.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/biodbMirbase.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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 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  [03:44:59.780] Loading definitions from package biodb version 1.8.0.
INFO  [03:45:02.314] Loading definitions from package biodbChebi version 1.6.0.
INFO  [03:45:02.368] Loading definitions from package biodbExpasy version 1.4.0.
INFO  [03:45:02.378] Loading definitions from package biodbHmdb version 1.6.0.
INFO  [03:45:02.415] Loading definitions from package biodbKegg version 1.6.0.
INFO  [03:45:02.473] Loading definitions from package biodbLipidmaps version 1.6.0.
INFO  [03:45:02.485] Loading definitions from package biodbMirbase version 1.4.0.
INFO  [03:45:02.499] Loading definitions from package biodbNcbi version 1.4.0.
INFO  [03:45:02.543] Loading definitions from package biodbNci version 1.4.0.
INFO  [03:45:02.554] Loading definitions from package biodbUniprot version 1.6.0.
> 
> # Get a connector:
> conn <- mybiodb$getFactory()$createConn('mirbase.mature')
> 
> # Get the first entry
> e <- conn$getEntry('MIMAT0000433')
INFO  [03:45:02.647] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/mirbase.mature-ecbae556d51779d9d48125ba5a617e19" for "mirbase.mature-ecbae556d51779d9d48125ba5a617e19".
INFO  [03:45:02.649] Downloading whole database of mirbase.mature.
trying URL 'https://www.mirbase.org/ftp/CURRENT/mature.fa.gz'
Warning in utils::download.file(url = url, destfile = dest.file, mode = "wb",  :
  downloaded length 0 != reported length 0
Warning in utils::download.file(url = url, destfile = dest.file, mode = "wb",  :
  cannot open URL 'https://www.mirbase.org/ftp/CURRENT/mature.fa.gz': HTTP status was '404 Not Found'
Error in utils::download.file(url = url, destfile = dest.file, mode = "wb",  : 
  cannot open URL 'https://www.mirbase.org/ftp/CURRENT/mature.fa.gz'
Calls: <Anonymous> ... <Anonymous> -> <Anonymous> -> <Anonymous> -> <Anonymous>
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
      method = "auto", cacheOK = FALSE, quiet = FALSE)`: cannot open URL 'https://www.mirbase.org/ftp/CURRENT/mature.fa.gz'
  Backtrace:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<MrbsMtrC>`)
   3.   └─conn$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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs
See
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/biodbMirbase.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL biodbMirbase
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘biodbMirbase’ ...
** 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 (biodbMirbase)

R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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/ftp/CURRENT/mature.fa.gz'
trying URL 'https://www.mirbase.org/ftp/CURRENT/mature.fa.gz'
trying URL 'https://www.mirbase.org/ftp/CURRENT/mature.fa.gz'
trying URL 'https://www.mirbase.org/ftp/CURRENT/mature.fa.gz'
trying URL 'https://www.mirbase.org/ftp/CURRENT/mature.fa.gz'
trying URL 'https://www.mirbase.org/ftp/CURRENT/mature.fa.gz'
[ FAIL 8 | WARN 12 | SKIP 0 | PASS 41 ]

══ 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/ftp/CURRENT/mature.fa.gz'
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$downloadFile(url = gz.url, dest.file = self$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/ftp/CURRENT/mature.fa.gz'
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 = gz.url, dest.file = self$getDownloadPath())
 11.                   └─utils::download.file(...)
── Failure (???): The entry page URL can be downloaded. ────────────────────────
!is.na(content) is not TRUE

`actual`:       
`expected`: TRUE
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<MrbsMtrC>`, opt = `<named list>`)
 3.   └─testthat::expect_true(!is.na(content))
── Failure (???): The entry page URL can be downloaded. ────────────────────────
nchar(content) > 0 is not TRUE

`actual`:       
`expected`: TRUE
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<MrbsMtrC>`, opt = `<named list>`)
 3.   └─testthat::expect_true(nchar(content) > 0)
── 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/ftp/CURRENT/mature.fa.gz'
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 = gz.url, dest.file = self$getDownloadPath())
 9.               └─utils::download.file(...)
── Error (???): One wrong entry does not block the retrieval of good ones ──────
Error in `utils::download.file(url = url, destfile = dest.file, mode = "wb", 
    method = "auto", cacheOK = FALSE, quiet = FALSE)`: cannot open URL 'https://www.mirbase.org/ftp/CURRENT/mature.fa.gz'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<MrbsMtrC>`, opt = `<named list>`)
 3.   └─biodb$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$downloadFile(url = gz.url, dest.file = self$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/ftp/CURRENT/mature.fa.gz'
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 = gz.url, dest.file = self$getDownloadPath())
 9.               └─utils::download.file(...)
── Error (???): We can get a list of entry ids. ────────────────────────────────
Error in `utils::download.file(url = url, destfile = dest.file, mode = "wb", 
    method = "auto", cacheOK = FALSE, quiet = FALSE)`: cannot open URL 'https://www.mirbase.org/ftp/CURRENT/mature.fa.gz'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<MrbsMtrC>`)
 3.   └─conn$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