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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:regutools.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings regutools_1.17.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/regutools.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 ‘regutools/DESCRIPTION’ ... OK
* this is package ‘regutools’ version ‘1.17.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ‘regutools’ 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 ... 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 ‘regutools-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: build_condition
> ### Title: Construct logical condition to query database
> ### Aliases: build_condition
> 
> ### ** Examples
> 
> 
> ## Connect to the RegulonDB database if necessary
> if (!exists("regulondb_conn")) regulondb_conn <- connect_database()
adding rname 'https://www.dropbox.com/s/ufp6wqcv5211v1w/regulondb_v10.8_sqlite.db?dl=1'
Warning in value[[3L]](cond) : 
trying to add rname 'https://www.dropbox.com/s/ufp6wqcv5211v1w/regulondb_v10.8_sqlite.db?dl=1' produced error:
  HTTP/2 stream 1 was not closed cleanly: PROTOCOL_ERROR (err 1)
Error in BiocFileCache::bfcrpath(bfc, url) : 
  not all 'rnames' found or unique.
Calls: connect_database -> <Anonymous> -> <Anonymous>
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:
      ▆
   1. └─regutools::connect_database() at test_convert_granges.R:62:11
   2.   ├─BiocFileCache::bfcrpath(bfc, url)
   3.   └─BiocFileCache::bfcrpath(bfc, url)
  ── Error ('test_network_functions.R:5:11'): Functions to retrieve gene regulation work as expected ──
  Error in `BiocFileCache::bfcrpath(bfc, url)`: not all 'rnames' found or unique.
  Backtrace:
      ▆
   1. └─regutools::connect_database() at test_network_functions.R:5:11
   2.   ├─BiocFileCache::bfcrpath(bfc, url)
   3.   └─BiocFileCache::bfcrpath(bfc, url)
  
  [ FAIL 16 | WARN 16 | SKIP 0 | PASS 3 ]
  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
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/regutools.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL regutools
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘regutools’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (regutools)

R version 4.4.1 (2024-06-14) -- "Race for Your Life"
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("regutools")
> 
> test_check("regutools")
[ FAIL 16 | WARN 16 | SKIP 0 | PASS 3 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-build_condition.R:5:11'): Test that the logical conditions its made as expected ──
Error in `BiocFileCache::bfcrpath(bfc, url)`: not all 'rnames' found or unique.
Backtrace:
    ▆
 1. └─regutools::connect_database() at test-build_condition.R:5:11
 2.   ├─BiocFileCache::bfcrpath(bfc, url)
 3.   └─BiocFileCache::bfcrpath(bfc, url)
── Error ('test-existing_intervals.R:6:11'): existing_intervals returns an expected value ──
Error in `BiocFileCache::bfcrpath(bfc, url)`: not all 'rnames' found or unique.
Backtrace:
    ▆
 1. └─regutools::connect_database() at test-existing_intervals.R:6:11
 2.   ├─BiocFileCache::bfcrpath(bfc, url)
 3.   └─BiocFileCache::bfcrpath(bfc, url)
── Error ('test-existing_partial_match.R:6:11'): existing_partial_match returns an expected value ──
Error in `BiocFileCache::bfcrpath(bfc, url)`: not all 'rnames' found or unique.
Backtrace:
    ▆
 1. └─regutools::connect_database() at test-existing_partial_match.R:6:11
 2.   ├─BiocFileCache::bfcrpath(bfc, url)
 3.   └─BiocFileCache::bfcrpath(bfc, url)
── Error ('test-get_binding_sites.R:5:11'): Function to get transcription factor binding sites works as expected ──
Error in `BiocFileCache::bfcrpath(bfc, url)`: not all 'rnames' found or unique.
Backtrace:
    ▆
 1. └─regutools::connect_database() at test-get_binding_sites.R:5:11
 2.   ├─BiocFileCache::bfcrpath(bfc, url)
 3.   └─BiocFileCache::bfcrpath(bfc, url)
── Error ('test-get_dataset.R:5:11'): Function get dataset works as expected ───
Error in `BiocFileCache::bfcrpath(bfc, url)`: not all 'rnames' found or unique.
Backtrace:
    ▆
 1. └─regutools::connect_database() at test-get_dataset.R:5:11
 2.   ├─BiocFileCache::bfcrpath(bfc, url)
 3.   └─BiocFileCache::bfcrpath(bfc, url)
── Error ('test-get_dna_objects.R:5:11'): output is a GRanges object ───────────
Error in `BiocFileCache::bfcrpath(bfc, url)`: not all 'rnames' found or unique.
Backtrace:
    ▆
 1. └─regutools::connect_database() at test-get_dna_objects.R:5:11
 2.   ├─BiocFileCache::bfcrpath(bfc, url)
 3.   └─BiocFileCache::bfcrpath(bfc, url)
── Error ('test-get_gene_regulators.R:5:11'): function get_gene_regulators works as expected ──
Error in `BiocFileCache::bfcrpath(bfc, url)`: not all 'rnames' found or unique.
Backtrace:
    ▆
 1. └─regutools::connect_database() at test-get_gene_regulators.R:5:11
 2.   ├─BiocFileCache::bfcrpath(bfc, url)
 3.   └─BiocFileCache::bfcrpath(bfc, url)
── Error ('test-get_gene_synonyms.R:4:11'): get_gene_synonyms works  ───────────
Error in `BiocFileCache::bfcrpath(bfc, url)`: not all 'rnames' found or unique.
Backtrace:
    ▆
 1. └─regutools::connect_database() at test-get_gene_synonyms.R:4:11
 2.   ├─BiocFileCache::bfcrpath(bfc, url)
 3.   └─BiocFileCache::bfcrpath(bfc, url)
── Error ('test-guess_id.R:4:11'): guess_id works  ─────────────────────────────
Error in `BiocFileCache::bfcrpath(bfc, url)`: not all 'rnames' found or unique.
Backtrace:
    ▆
 1. └─regutools::connect_database() at test-guess_id.R:4:11
 2.   ├─BiocFileCache::bfcrpath(bfc, url)
 3.   └─BiocFileCache::bfcrpath(bfc, url)
── Error ('test-list_attributes.R:5:11'): list_attributes works as expected  ───
Error in `BiocFileCache::bfcrpath(bfc, url)`: not all 'rnames' found or unique.
Backtrace:
    ▆
 1. └─regutools::connect_database() at test-list_attributes.R:5:11
 2.   ├─BiocFileCache::bfcrpath(bfc, url)
 3.   └─BiocFileCache::bfcrpath(bfc, url)
── Error ('test-list_datasets.R:5:11'): function list_dataset works as expected ──
Error in `BiocFileCache::bfcrpath(bfc, url)`: not all 'rnames' found or unique.
Backtrace:
    ▆
 1. └─regutools::connect_database() at test-list_datasets.R:5:11
 2.   ├─BiocFileCache::bfcrpath(bfc, url)
 3.   └─BiocFileCache::bfcrpath(bfc, url)
── Error ('test-non_existing_intervals.R:6:11'): existing_partial_match returns an expected value ──
Error in `BiocFileCache::bfcrpath(bfc, url)`: not all 'rnames' found or unique.
Backtrace:
    ▆
 1. └─regutools::connect_database() at test-non_existing_intervals.R:6:11
 2.   ├─BiocFileCache::bfcrpath(bfc, url)
 3.   └─BiocFileCache::bfcrpath(bfc, url)
── Error ('test-plot_dna_objects.R:5:11'): non-valid genomic elements causes error ──
Error in `BiocFileCache::bfcrpath(bfc, url)`: not all 'rnames' found or unique.
Backtrace:
    ▆
 1. └─regutools::connect_database() at test-plot_dna_objects.R:5:11
 2.   ├─BiocFileCache::bfcrpath(bfc, url)
 3.   └─BiocFileCache::bfcrpath(bfc, url)
── Error ('test_convert_granges.R:5:11'): Results from regulondb queries can be converted to GRanges ──
Error in `BiocFileCache::bfcrpath(bfc, url)`: not all 'rnames' found or unique.
Backtrace:
    ▆
 1. └─regutools::connect_database() at test_convert_granges.R:5:11
 2.   ├─BiocFileCache::bfcrpath(bfc, url)
 3.   └─BiocFileCache::bfcrpath(bfc, url)
── Error ('test_convert_granges.R:62:11'): Results from regulondb queries can be converted to Biostrings ──
Error in `BiocFileCache::bfcrpath(bfc, url)`: not all 'rnames' found or unique.
Backtrace:
    ▆
 1. └─regutools::connect_database() at test_convert_granges.R:62:11
 2.   ├─BiocFileCache::bfcrpath(bfc, url)
 3.   └─BiocFileCache::bfcrpath(bfc, url)
── Error ('test_network_functions.R:5:11'): Functions to retrieve gene regulation work as expected ──
Error in `BiocFileCache::bfcrpath(bfc, url)`: not all 'rnames' found or unique.
Backtrace:
    ▆
 1. └─regutools::connect_database() at test_network_functions.R:5:11
 2.   ├─BiocFileCache::bfcrpath(bfc, url)
 3.   └─BiocFileCache::bfcrpath(bfc, url)

[ FAIL 16 | WARN 16 | SKIP 0 | PASS 3 ]
Error: Test failures
Execution halted