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###
### Running command:
###
###   E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BiocFileCache.install-out.txt --library=E:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings BiocFileCache_2.12.0.tar.gz
###
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* using log directory 'E:/biocbuild/bbs-3.19-bioc/meat/BiocFileCache.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'BiocFileCache/DESCRIPTION' ... OK
* this is package 'BiocFileCache' version '2.12.0'
* 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 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 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 ... NOTE
.sql_clean_cache: no visible binding for global variable 'rid'
.sql_clean_cache: no visible binding for global variable 'access_time'
.sql_get_resource_table: no visible binding for global variable 'rid'
.sql_get_resource_table: no visible binding for global variable 'id'
Undefined global functions or variables:
  access_time id rid
* checking Rd files ... NOTE
checkRd: (-1) BiocFileCache-class.Rd:486-487: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BiocFileCache-class.Rd:488: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BiocFileCache-class.Rd:495-496: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BiocFileCache-class.Rd:497-500: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BiocFileCache-class.Rd:501: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BiocFileCache-class.Rd:502-504: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BiocFileCache-class.Rd:505-506: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BiocFileCache-class.Rd:507-508: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BiocFileCache-class.Rd:509-511: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BiocFileCache-class.Rd:512-516: Lost braces in \itemize; meant \describe ?
* 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] "E:\\biocbuild\\bbs-3.19-bioc\\tmpdir\\RtmpATF2Wy\\file110c6d1d86e"
> length(bfc0)
[1] 0
> path <- bfcnew(bfc0, "NewResource")
> path
                                                                                         BFC1 
"E:\\biocbuild\\bbs-3.19-bioc\\tmpdir\\RtmpATF2Wy\\file110c6d1d86e/110c4810781b_110c4810781b" 
> fl1 <- tempfile(); file.create(fl1)
[1] TRUE
> bfcadd(bfc0, "Test1", fl1)                 # copy
                                                                                             BFC2 
"E:\\biocbuild\\bbs-3.19-bioc\\tmpdir\\RtmpATF2Wy\\file110c6d1d86e/110c704a772a_file110c701730f7" 
> fl2 <- tempfile(); file.create(fl2)
[1] TRUE
> bfcadd(bfc0, "Test2", fl2, action="move")         # move
                                                                                             BFC3 
"E:\\biocbuild\\bbs-3.19-bioc\\tmpdir\\RtmpATF2Wy\\file110c6d1d86e/110c246f428c_file110c73f46985" 
> fl3 <- tempfile(); file.create(fl3)
[1] TRUE
> add3 <- bfcadd(bfc0, "Test3", fl3, rtype="local", action="asis")  # reference
> rid3 <- names(add3)
> 
> bfc0
class: BiocFileCache
bfccache: E:\biocbuild\bbs-3.19-bioc\tmpdir\RtmpATF2Wy\file110c6d1d86e
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 <- "http://httpbin.org/get"
> bfcadd(bfc0, "TestWeb", fpath=url)
Warning: download failed
  web resource path: 'http://httpbin.org/get'
  local file path: 'E:\biocbuild\bbs-3.19-bioc\tmpdir\RtmpATF2Wy\file110c6d1d86e/110c3dd54975_get'
  reason: Service Unavailable (HTTP 503).
Warning: bfcadd() failed; resource removed
  rid: BFC5
  fpath: 'http://httpbin.org/get'
  reason: download failed
Error in .util_download(x, rid[i], proxy, 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:
  ── Error ('test_BiocFileCache_class.R:182:1'): (code run outside of `test_that()`) ──
  Error in `.util_download(x, rid[i], proxy, 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 2 NOTEs
See
  'E:/biocbuild/bbs-3.19-bioc/meat/BiocFileCache.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL BiocFileCache
###
##############################################################################
##############################################################################


* installing to library 'E:/biocbuild/bbs-3.19-bioc/R/library'
* installing *source* package 'BiocFileCache' ...
** 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 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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, 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, 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