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###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:bugsigdbr.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings bugsigdbr_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/bugsigdbr.Rcheck'
* using R version 4.5.0 RC (2025-04-04 r88126 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'bugsigdbr/DESCRIPTION' ... OK
* this is package 'bugsigdbr' version '1.14.0'
* 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 '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 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 5.61   0.53    6.41
subsetByOntology 4.59   0.86    5.86
* 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:
    5.         ├─DBI::dbExecute(con, sql, params = param)
    6.         └─DBI::dbExecute(con, sql, params = param)
    7.           ├─DBI::dbSendStatement(conn, statement, ...)
    8.           └─DBI::dbSendStatement(conn, statement, ...)
    9.             ├─DBI::dbSendQuery(conn, statement, ...)
   10.             └─RSQLite::dbSendQuery(conn, statement, ...)
   11.               └─RSQLite (local) .local(conn, statement, ...)
   12.                 ├─DBI::dbBind(rs, params)
   13.                 └─RSQLite::dbBind(rs, params)
   14.                   └─RSQLite:::db_bind(res, as.list(params), ..., allow_named_superset = FALSE)
   15.                     └─RSQLite:::result_bind(res@ptr, params)
  
  [ FAIL 5 | WARN 0 | SKIP 0 | PASS 117 ]
  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: 1 ERROR, 2 NOTEs
See
  'E:/biocbuild/bbs-3.21-bioc/meat/bugsigdbr.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL bugsigdbr
###
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* installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library'
* installing *source* package 'bugsigdbr' ...
** this is package 'bugsigdbr' version '1.14.0'
** 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 (bugsigdbr)

R version 4.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six"
Copyright (C) 2025 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(bugsigdbr)
> 
> test_check("bugsigdbr")
[ FAIL 5 | WARN 0 | SKIP 0 | PASS 117 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── 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-importBugSigDB.R:27:5'): importBugSigDB from the edge (devel) ──
Error: database or disk is full
Backtrace:
     ▆
  1. └─bugsigdbr::importBugSigDB(version = "devel", cache = FALSE) at test-importBugSigDB.R:27:5
  2.   └─bugsigdbr:::.cacheResource(rname, url, download = FALSE, ext = ".rds")
  3.     ├─BiocFileCache::bfcremove(bfc, qgsc$rid)
  4.     └─BiocFileCache::bfcremove(bfc, qgsc$rid)
  5.       └─BiocFileCache:::.sql_remove_resource(x, rids)
  6.         └─BiocFileCache:::.sql_db_execute(bfc, cmd)
  7.           ├─DBI::dbExecute(con, sql, params = param)
  8.           └─DBI::dbExecute(con, sql, params = param)
  9.             ├─DBI::dbSendStatement(conn, statement, ...)
 10.             └─DBI::dbSendStatement(conn, statement, ...)
 11.               ├─DBI::dbSendQuery(conn, statement, ...)
 12.               └─RSQLite::dbSendQuery(conn, statement, ...)
 13.                 └─RSQLite (local) .local(conn, statement, ...)
 14.                   ├─methods::new(...)
 15.                   │ ├─methods::initialize(value, ...)
 16.                   │ └─methods::initialize(value, ...)
 17.                   └─RSQLite:::result_create(conn@ptr, statement)
── Error ('test-importBugSigDB.R:33:5'): importBugSigDB from github hash ───────
Error: database or disk is full
Backtrace:
     ▆
  1. └─bugsigdbr::importBugSigDB(version = "30383a9", cache = FALSE) at test-importBugSigDB.R:33:5
  2.   └─bugsigdbr:::.cacheResource(rname, url, download = FALSE, ext = ".rds")
  3.     ├─BiocFileCache::bfcremove(bfc, qgsc$rid)
  4.     └─BiocFileCache::bfcremove(bfc, qgsc$rid)
  5.       └─BiocFileCache:::.sql_remove_resource(x, rids)
  6.         └─BiocFileCache:::.sql_db_execute(bfc, cmd)
  7.           ├─DBI::dbExecute(con, sql, params = param)
  8.           └─DBI::dbExecute(con, sql, params = param)
  9.             ├─DBI::dbSendStatement(conn, statement, ...)
 10.             └─DBI::dbSendStatement(conn, statement, ...)
 11.               ├─DBI::dbSendQuery(conn, statement, ...)
 12.               └─RSQLite::dbSendQuery(conn, statement, ...)
 13.                 └─RSQLite (local) .local(conn, statement, ...)
 14.                   ├─methods::new(...)
 15.                   │ ├─methods::initialize(value, ...)
 16.                   │ └─methods::initialize(value, ...)
 17.                   └─RSQLite:::result_create(conn@ptr, statement)
── Error ('test-ontology.R:3:1'): (code run outside of `test_that()`) ──────────
Error: database or disk is full
Backtrace:
     ▆
  1. └─bugsigdbr::importBugSigDB() at test-ontology.R:3:1
  2.   └─bugsigdbr:::.getResourceFromCache(rname, FUN = .getdf)
  3.     └─BiocFileCache:::.sql_set_expires(bfc, rid, NA)
  4.       └─BiocFileCache:::.sql_db_execute(bfc, sql, rid = rid, expires = expires)
  5.         ├─DBI::dbExecute(con, sql, params = param)
  6.         └─DBI::dbExecute(con, sql, params = param)
  7.           ├─DBI::dbSendStatement(conn, statement, ...)
  8.           └─DBI::dbSendStatement(conn, statement, ...)
  9.             ├─DBI::dbSendQuery(conn, statement, ...)
 10.             └─RSQLite::dbSendQuery(conn, statement, ...)
 11.               └─RSQLite (local) .local(conn, statement, ...)
 12.                 ├─DBI::dbBind(rs, params)
 13.                 └─RSQLite::dbBind(rs, params)
 14.                   └─RSQLite:::db_bind(res, as.list(params), ..., allow_named_superset = FALSE)
 15.                     └─RSQLite:::result_bind(res@ptr, params)
── Error ('test-restrictTaxLevel.R:1:1'): (code run outside of `test_that()`) ──
Error: database or disk is full
Backtrace:
     ▆
  1. └─bugsigdbr::importBugSigDB() at test-restrictTaxLevel.R:1:1
  2.   └─bugsigdbr:::.getResourceFromCache(rname, FUN = .getdf)
  3.     └─BiocFileCache:::.sql_set_expires(bfc, rid, NA)
  4.       └─BiocFileCache:::.sql_db_execute(bfc, sql, rid = rid, expires = expires)
  5.         ├─DBI::dbExecute(con, sql, params = param)
  6.         └─DBI::dbExecute(con, sql, params = param)
  7.           ├─DBI::dbSendStatement(conn, statement, ...)
  8.           └─DBI::dbSendStatement(conn, statement, ...)
  9.             ├─DBI::dbSendQuery(conn, statement, ...)
 10.             └─RSQLite::dbSendQuery(conn, statement, ...)
 11.               └─RSQLite (local) .local(conn, statement, ...)
 12.                 ├─DBI::dbBind(rs, params)
 13.                 └─RSQLite::dbBind(rs, params)
 14.                   └─RSQLite:::db_bind(res, as.list(params), ..., allow_named_superset = FALSE)
 15.                     └─RSQLite:::result_bind(res@ptr, params)

[ FAIL 5 | WARN 0 | SKIP 0 | PASS 117 ]
Error: Test failures
Execution halted