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###
### Running command:
###
###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/R CMD check --install=check:BiocFileCache.install-out.txt --library=/home/rapidbuild/bbs-3.23-bioc-rapid/R/site-library --timings BiocFileCache_3.1.0.tar.gz
###
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* using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/BiocFileCache.Rcheck’
* using R Under development (unstable) (2025-10-28 r88973)
* 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 ‘3.1.0’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Lori Shepherd <lori.shepherd@roswellpark.org>’

Unknown, possibly misspelled, fields in DESCRIPTION:
  ‘DevelopmentURL’ ‘git_url’ ‘git_branch’ ‘git_last_commit’ ‘git_last_commit_date’

The Description field should not start with the package name,
  'This package' or similar.
* 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 use of S3 registration ... 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 ‘BiocFileCache-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: BiocFileCache-class
> ### Title: BiocFileCache class
> ### Aliases: BiocFileCache-class BiocFileCache
> ###   bfccache,BiocFileCacheBase-method bfccache bfccache,missing-method
> ###   length,BiocFileCacheBase-method bfcrid bfcrid,missing-method
> ###   bfcrid,BiocFileCacheReadOnly-method bfcrid,BiocFileCache-method
> ###   [,BiocFileCache,character,missing-method
> ###   [,BiocFileCacheReadOnly,character,missing-method
> ###   [,BiocFileCache,missing,missing-method
> ###   [,BiocFileCacheReadOnly,missing,missing-method
> ###   [[,BiocFileCacheBase,character,missing-method
> ###   [[<-,BiocFileCache,character,missing,character-method
> ###   bfcnew,missing-method bfcnew,BiocFileCache-method bfcnew
> ###   bfcadd,missing-method bfcadd,BiocFileCache-method bfcadd
> ###   bfcinfo,missing-method bfcinfo,BiocFileCacheBase-method bfcinfo
> ###   bfcrid,tbl_bfc-method bfcpath,missing-method
> ###   bfcpath,BiocFileCacheBase-method bfcpath bfcrpath,missing-method
> ###   bfcrpath,BiocFileCacheBase-method bfcrpath bfcupdate,missing-method
> ###   bfcupdate,BiocFileCache-method bfcupdate bfcmeta<-
> ###   bfcmeta<-,BiocFileCacheBase-method bfcmetaremove,missing-method
> ###   bfcmetaremove,BiocFileCacheBase-method bfcmetaremove
> ###   bfcmetalist,missing-method bfcmetalist,BiocFileCacheBase-method
> ###   bfcmetalist bfcmeta,missing-method bfcmeta,BiocFileCacheBase-method
> ###   bfcmeta bfcquerycols,missing-method
> ###   bfcquerycols,BiocFileCacheBase-method bfcquerycols
> ###   bfcquery,missing-method bfcquery,BiocFileCacheBase-method bfcquery
> ###   bfccount,missing-method bfccount,BiocFileCacheBase-method bfccount
> ###   bfccount,tbl_bfc-method bfcneedsupdate,missing-method
> ###   bfcneedsupdate,BiocFileCacheBase-method bfcneedsupdate
> ###   bfcdownload,missing-method bfcdownload,BiocFileCache-method
> ###   bfcdownload bfcremove,missing-method bfcremove,BiocFileCache-method
> ###   bfcremove bfcsync,missing-method bfcsync,BiocFileCache-method bfcsync
> ###   exportbfc,missing-method exportbfc,BiocFileCacheBase-method exportbfc
> ###   importbfc,character-method importbfc cleanbfc,missing-method
> ###   cleanbfc,BiocFileCache-method cleanbfc removebfc,missing-method
> ###   removebfc,BiocFileCache-method removebfc
> ###   show,BiocFileCacheBase-method
> 
> ### ** Examples
> 
> # bfc <- BiocFileCache()            # global cache
> # bfc
> bfc0 <- BiocFileCache(tempfile())         # temporary catch for examples
> bfccache(bfc0)
[1] "/tmp/RtmppbOrqE/file27bbe31617eadb"
> length(bfc0)
[1] 0
> path <- bfcnew(bfc0, "NewResource")
> path
                                                              BFC1 
"/tmp/RtmppbOrqE/file27bbe31617eadb/27bbe3394e0fe9_27bbe3394e0fe9" 
> fl1 <- tempfile(); file.create(fl1)
[1] TRUE
> bfcadd(bfc0, "Test1", fl1)                 # copy
                                                                 BFC2 
"/tmp/RtmppbOrqE/file27bbe31617eadb/27bbe3422ef4b2_file27bbe3496fd49" 
> fl2 <- tempfile(); file.create(fl2)
[1] TRUE
> bfcadd(bfc0, "Test2", fl2, action="move")         # move
                                                                  BFC3 
"/tmp/RtmppbOrqE/file27bbe31617eadb/27bbe357d1859b_file27bbe36a357c32" 
> fl3 <- tempfile(); file.create(fl3)
[1] TRUE
> add3 <- bfcadd(bfc0, "Test3", fl3, rtype="local", action="asis")  # reference
> rid3 <- names(add3)
> 
> bfc0
class: BiocFileCache
bfccache: /tmp/RtmppbOrqE/file27bbe31617eadb
bfccount: 4
For more information see: bfcinfo() or bfcquery()
> file.exists(fl1)                                # TRUE
[1] TRUE
> file.exists(fl2)                                # FALSE
[1] FALSE
> file.exists(fl3)                                # TRUE
[1] TRUE
> 
> # add a remote resource
> url <- "https://httpbin.org/get"
> bfcadd(bfc0, "TestWeb", fpath=url)
Warning: download failed
  web resource path: ‘https://httpbin.org/get’
  local file path: ‘/tmp/RtmppbOrqE/file27bbe31617eadb/27bbe32df8e262_get’
  reason: HTTP 503 Service Unavailable.
Warning: bfcadd() failed; resource removed
  rid: BFC5
  fpath: ‘https://httpbin.org/get’
  reason: download failed
Error in .util_download(x, rid[i], proxy, progress, config, "bfcadd()",  : 
  bfcadd() failed; see warnings()
Calls: bfcadd -> bfcadd -> .util_download
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:
  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 ──
  Expected `length(list.files(bfccache(newbfc)))` to be identical to 2L.
  Differences:
  1/1 mismatches
  [1] 3 - 2 == 1
  
  [ FAIL 3 | WARN 4 | SKIP 1 | 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: 3 ERRORs, 1 NOTE
See
  ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/BiocFileCache.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/R CMD INSTALL BiocFileCache
###
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* installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library’
* installing *source* package ‘BiocFileCache’ ...
** this is package ‘BiocFileCache’ version ‘3.1.0’
** 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 Under development (unstable) (2025-10-28 r88973) -- "Unsuffered Consequences"
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")
Saving _problems/test_BiocFileCache_class-44.R
Saving _problems/test_BiocFileCache_class-182.R

Saving _problems/test_makeBiocFileCacheFromDataFrame-70.R

[ FAIL 3 | WARN 4 | SKIP 1 | PASS 85 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1):

══ 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 ──
Expected `length(list.files(bfccache(newbfc)))` to be identical to 2L.
Differences:
1/1 mismatches
[1] 3 - 2 == 1

[ FAIL 3 | WARN 4 | SKIP 1 | PASS 85 ]
Error:
! Test failures.
Execution halted