##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:bugsigdbr.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings bugsigdbr_1.16.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/bugsigdbr.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘bugsigdbr/DESCRIPTION’ ... OK
* this is package ‘bugsigdbr’ version ‘1.16.2’
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
restrictTaxLevel  6.726  0.158   7.402
subsetByOntology  6.517  0.300  13.144
getMetaSignatures 3.422  0.125  46.717
getSignatures     1.632  0.097  31.805
writeGMT          1.667  0.024   7.803
importBugSigDB    0.595  0.024  27.543
* 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 in `open.connection(structure(4L, class = c("curl", "connection"), conn_id = <pointer: 0x60d684fc3260>), "rb")`: cannot open the connection
  Backtrace:
      ▆
   1. ├─bugsigdbr (local) checkImport(bsdb, url, nrows = 3500) at test-importBugSigDB.R:23:5
   2. │ ├─base::suppressWarnings(...) at test-importBugSigDB.R:8:5
   3. │ │ └─base::withCallingHandlers(...)
   4. │ └─vroom::vroom(url, skip = 1L, progress = FALSE, show_col_types = FALSE)
   5. │   └─vroom:::vroom_(...)
   6. ├─base (local) `<fn>`(`<curl>`, "rb")
   7. └─base::open.connection(`<curl>`, "rb")
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 225 ]
  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 bugsigdbr.Rmd:73-77 [getBugSigDB]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! download failed; see warnings()
---
Backtrace:
    ▆
 1. └─bugsigdbr::importBugSigDB()
 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: 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: 2 ERRORs, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/bugsigdbr.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL bugsigdbr
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘bugsigdbr’ ...
** this is package ‘bugsigdbr’ version ‘1.16.2’
** 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 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 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")

Saving _problems/test-importBugSigDB-23.R


[ FAIL 1 | WARN 0 | SKIP 0 | PASS 225 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-importBugSigDB.R:23:5'): importBugSigDB from Zenodo ────────────
Error in `open.connection(structure(4L, class = c("curl", "connection"), conn_id = <pointer: 0x60d684fc3260>), "rb")`: cannot open the connection
Backtrace:
    ▆
 1. ├─bugsigdbr (local) checkImport(bsdb, url, nrows = 3500) at test-importBugSigDB.R:23:5
 2. │ ├─base::suppressWarnings(...) at test-importBugSigDB.R:8:5
 3. │ │ └─base::withCallingHandlers(...)
 4. │ └─vroom::vroom(url, skip = 1L, progress = FALSE, show_col_types = FALSE)
 5. │   └─vroom:::vroom_(...)
 6. ├─base (local) `<fn>`(`<curl>`, "rb")
 7. └─base::open.connection(`<curl>`, "rb")

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 225 ]
Error:
! Test failures.
Execution halted