##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:bugsigdbr.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings bugsigdbr_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/bugsigdbr.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘bugsigdbr/DESCRIPTION’ ... OK
* this is package ‘bugsigdbr’ version ‘1.12.0’
* 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 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 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
subsetByOntology  7.883  0.515   9.106
restrictTaxLevel  7.367  0.509   8.972
getMetaSignatures 5.262  0.241   6.501
* 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: 0x7fc34b752c90>), 
      "rb")`: cannot open the connection
  Backtrace:
      ▆
   1. ├─bugsigdbr (local) checkImport(bsdb, url, nrows = 5450) at test-importBugSigDB.R:29:5
   2. │ ├─base::suppressWarnings(...) at test-importBugSigDB.R:8:5
   3. │ │ └─base::withCallingHandlers(...)
   4. │ └─vroom::vroom(url, skip = 1L, progress = FALSE, show_col_types = FALSE) at test-importBugSigDB.R:8:5
   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 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
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/bugsigdbr.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL bugsigdbr
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘bugsigdbr’ ...
** 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 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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 1 | WARN 0 | SKIP 0 | PASS 225 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-importBugSigDB.R:29:5'): importBugSigDB from the edge (devel) ──
Error in `open.connection(structure(4L, class = c("curl", "connection"), conn_id = <pointer: 0x7fc34b752c90>), 
    "rb")`: cannot open the connection
Backtrace:
    ▆
 1. ├─bugsigdbr (local) checkImport(bsdb, url, nrows = 5450) at test-importBugSigDB.R:29:5
 2. │ ├─base::suppressWarnings(...) at test-importBugSigDB.R:8:5
 3. │ │ └─base::withCallingHandlers(...)
 4. │ └─vroom::vroom(url, skip = 1L, progress = FALSE, show_col_types = FALSE) at test-importBugSigDB.R:8:5
 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