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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:bugsigdbr.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings bugsigdbr_1.10.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/bugsigdbr.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 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘bugsigdbr/DESCRIPTION’ ... OK
* this is package ‘bugsigdbr’ 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 ‘bugsigdbr’ 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 dependencies in R code ... NOTE
Unexported object imported by a ':::' call: ‘BiocFileCache:::.sql_set_expires’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
getMetaSignatures: no visible binding for global variable ‘Abundance in
  Group 1’
Undefined global functions or variables:
  Abundance in Group 1
* 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 ‘bugsigdbr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: importBugSigDB
> ### Title: Obtain published microbial signatures from bugsigdb.org
> ### Aliases: importBugSigDB
> 
> ### ** Examples
> 
> 
>  df <- importBugSigDB()
Error: download failed; see warnings()
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:
  ── Error ('test-restrictTaxLevel.R:1:1'): (code run outside of `test_that()`) ──
  Error: download failed; see warnings()
  Backtrace:
      ▆
   1. └─bugsigdbr::importBugSigDB() at test-restrictTaxLevel.R:1:1
   2.   └─bugsigdbr:::.getResourceFromCache(rname, FUN = .getdf)
   3.     ├─base::suppressWarnings(...)
   4.     │ └─base::withCallingHandlers(...)
   5.     ├─BiocFileCache::bfcdownload(bfc, rid, ask = FALSE, ...)
   6.     └─BiocFileCache::bfcdownload(bfc, rid, ask = FALSE, ...)
   7.       └─BiocFileCache:::.util_download_and_rename(...)
  
  [ FAIL 5 | WARN 0 | SKIP 0 | PASS 34 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘bugsigdbr.Rmd’ using rmarkdown

Quitting from lines 74-77 [getBugSigDB] (bugsigdbr.Rmd)
Error: processing vignette 'bugsigdbr.Rmd' failed with diagnostics:
download failed; see warnings()
--- failed re-building ‘bugsigdbr.Rmd’

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

Error: Vignette re-building failed.
Execution halted

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

Status: 3 ERRORs, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/bugsigdbr.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL bugsigdbr
###
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* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘bugsigdbr’ ...
** 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 (bugsigdbr)

R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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.

> library(testthat)
> library(bugsigdbr)
> 
> test_check("bugsigdbr")
[ FAIL 5 | WARN 0 | SKIP 0 | PASS 34 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-getMetaSignatures.R:1:1'): (code run outside of `test_that()`) ──
Error: download failed; see warnings()
Backtrace:
    ▆
 1. └─bugsigdbr::importBugSigDB() at test-getMetaSignatures.R:1:1
 2.   └─bugsigdbr:::.getResourceFromCache(rname, FUN = .getdf)
 3.     ├─base::suppressWarnings(...)
 4.     │ └─base::withCallingHandlers(...)
 5.     ├─BiocFileCache::bfcdownload(bfc, rid, ask = FALSE, ...)
 6.     └─BiocFileCache::bfcdownload(bfc, rid, ask = FALSE, ...)
 7.       └─BiocFileCache:::.util_download_and_rename(...)
── Error ('test-getSignatures.R:1:1'): (code run outside of `test_that()`) ─────
Error: download failed; see warnings()
Backtrace:
    ▆
 1. └─bugsigdbr::importBugSigDB() at test-getSignatures.R:1:1
 2.   └─bugsigdbr:::.getResourceFromCache(rname, FUN = .getdf)
 3.     ├─base::suppressWarnings(...)
 4.     │ └─base::withCallingHandlers(...)
 5.     ├─BiocFileCache::bfcdownload(bfc, rid, ask = FALSE, ...)
 6.     └─BiocFileCache::bfcdownload(bfc, rid, ask = FALSE, ...)
 7.       └─BiocFileCache:::.util_download_and_rename(...)
── Error ('test-importBugSigDB.R:21:5'): importBugSigDB from Zenodo ────────────
Error: download failed; see warnings()
Backtrace:
    ▆
 1. └─bugsigdbr::importBugSigDB(...) at test-importBugSigDB.R:21:5
 2.   ├─base::suppressMessages(.getResourceFromCache(rname, FUN = .getdf))
 3.   │ └─base::withCallingHandlers(...)
 4.   └─bugsigdbr:::.getResourceFromCache(rname, FUN = .getdf)
 5.     ├─base::suppressWarnings(...)
 6.     │ └─base::withCallingHandlers(...)
 7.     ├─BiocFileCache::bfcdownload(bfc, rid, ask = FALSE, ...)
 8.     └─BiocFileCache::bfcdownload(bfc, rid, ask = FALSE, ...)
 9.       └─BiocFileCache:::.util_download_and_rename(...)
── Error ('test-ontology.R:3:1'): (code run outside of `test_that()`) ──────────
Error: download failed; see warnings()
Backtrace:
    ▆
 1. └─bugsigdbr::importBugSigDB() at test-ontology.R:3:1
 2.   └─bugsigdbr:::.getResourceFromCache(rname, FUN = .getdf)
 3.     ├─base::suppressWarnings(...)
 4.     │ └─base::withCallingHandlers(...)
 5.     ├─BiocFileCache::bfcdownload(bfc, rid, ask = FALSE, ...)
 6.     └─BiocFileCache::bfcdownload(bfc, rid, ask = FALSE, ...)
 7.       └─BiocFileCache:::.util_download_and_rename(...)
── Error ('test-restrictTaxLevel.R:1:1'): (code run outside of `test_that()`) ──
Error: download failed; see warnings()
Backtrace:
    ▆
 1. └─bugsigdbr::importBugSigDB() at test-restrictTaxLevel.R:1:1
 2.   └─bugsigdbr:::.getResourceFromCache(rname, FUN = .getdf)
 3.     ├─base::suppressWarnings(...)
 4.     │ └─base::withCallingHandlers(...)
 5.     ├─BiocFileCache::bfcdownload(bfc, rid, ask = FALSE, ...)
 6.     └─BiocFileCache::bfcdownload(bfc, rid, ask = FALSE, ...)
 7.       └─BiocFileCache:::.util_download_and_rename(...)

[ FAIL 5 | WARN 0 | SKIP 0 | PASS 34 ]
Error: Test failures
Execution halted