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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BiocFileCache.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BiocFileCache_3.0.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/BiocFileCache.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* 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 ‘BiocFileCache/DESCRIPTION’ ... OK
* this is package ‘BiocFileCache’ version ‘3.0.0’
* 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 ‘BiocFileCache’ 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 whether startup messages can be suppressed ... 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
BiocFileCache-class 3.113  0.261  20.353
* 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 `.util_download(x, rid[i], proxy, progress, config, "bfcadd()", 
      ...)`: bfcadd() failed; see warnings()
  Backtrace:
      ▆
   1. ├─BiocFileCache::bfcadd(bfc, "test-3", url, rtype = "web") at test_BiocFileCache_class.R:182:1
   2. └─BiocFileCache::bfcadd(bfc, "test-3", url, rtype = "web")
   3.   └─BiocFileCache:::.util_download(...)
  ── Failure ('test_makeBiocFileCacheFromDataFrame.R:70:5'): makeBiocFileCacheFromDataFrame works ──
  length(list.files(bfccache(newbfc))) not identical to 2L.
  1/1 mismatches
  [1] 3 - 2 == 1
  
  [ FAIL 3 | WARN 4 | SKIP 0 | PASS 85 ]
  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 ‘BiocFileCache.Rmd’ using rmarkdown

Quitting from BiocFileCache.Rmd:206-221 [bfcaddremote]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `.util_download()`:
! bfcadd() failed; see warnings()
---
Backtrace:
    ▆
 1. ├─BiocFileCache::bfcadd(bfc, "TestWeb", fpath = url)
 2. └─BiocFileCache::bfcadd(bfc, "TestWeb", fpath = url)
 3.   └─BiocFileCache:::.util_download(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'BiocFileCache.Rmd' failed with diagnostics:
bfcadd() failed; see warnings()
--- failed re-building ‘BiocFileCache.Rmd’

--- re-building ‘BiocFileCache_Troubleshooting.Rmd’ using rmarkdown
--- finished re-building ‘BiocFileCache_Troubleshooting.Rmd’

--- re-building ‘BiocFileCache_UseCases.Rmd’ using rmarkdown
--- finished re-building ‘BiocFileCache_UseCases.Rmd’

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

Error: Vignette re-building failed.
Execution halted

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

Status: 2 ERRORs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/BiocFileCache.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL BiocFileCache
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘BiocFileCache’ ...
** this is package ‘BiocFileCache’ version ‘3.0.0’
** 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 (BiocFileCache)

R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
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(BiocFileCache)
Loading required package: dbplyr
> 
> test_check("BiocFileCache")


[ FAIL 3 | WARN 4 | SKIP 0 | PASS 85 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_BiocFileCache_class.R:44:5'): bfcadd and bfcnew works ──────────
Error in `.util_download(x, rid[i], proxy, progress, config, "bfcadd()", 
    ...)`: bfcadd() failed; see warnings()
Backtrace:
    ▆
 1. ├─BiocFileCache::bfcadd(bfc, "test-4", url, rtype = "web") at test_BiocFileCache_class.R:44:5
 2. └─BiocFileCache::bfcadd(bfc, "test-4", url, rtype = "web")
 3.   └─BiocFileCache:::.util_download(...)
── Error ('test_BiocFileCache_class.R:182:1'): (code run outside of `test_that()`) ──
Error in `.util_download(x, rid[i], proxy, progress, config, "bfcadd()", 
    ...)`: bfcadd() failed; see warnings()
Backtrace:
    ▆
 1. ├─BiocFileCache::bfcadd(bfc, "test-3", url, rtype = "web") at test_BiocFileCache_class.R:182:1
 2. └─BiocFileCache::bfcadd(bfc, "test-3", url, rtype = "web")
 3.   └─BiocFileCache:::.util_download(...)
── Failure ('test_makeBiocFileCacheFromDataFrame.R:70:5'): makeBiocFileCacheFromDataFrame works ──
length(list.files(bfccache(newbfc))) not identical to 2L.
1/1 mismatches
[1] 3 - 2 == 1

[ FAIL 3 | WARN 4 | SKIP 0 | PASS 85 ]
Error: Test failures
Execution halted