R version 4.5.0 RC (2025-04-04 r88112 ucrt) -- "How About a Twenty-Six"
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Platform: x86_64-w64-mingw32/x64

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> # The bedr package is copyright (c) 2014 Ontario Institute for Cancer Research (OICR)
> # This package and its accompanying libraries is free software; you can redistribute it and/or modify it under the terms of the GPL
> # (either version 1, or at your option, any later version) or the Artistic License 2.0.  Refer to LICENSE for the full license text.
> # OICR makes no representations whatsoever as to the SOFTWARE contained herein.  It is experimental in nature and is provided WITHOUT
> # WARRANTY OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE OR ANY OTHER WARRANTY, EXPRESS OR IMPLIED. OICR MAKES NO REPRESENTATION
> # OR WARRANTY THAT THE USE OF THIS SOFTWARE WILL NOT INFRINGE ANY PATENT OR OTHER PROPRIETARY RIGHT.
> # By downloading this SOFTWARE, your Institution hereby indemnifies OICR against any loss, claim, damage or liability, of whatsoever kind or
> # nature, which may arise from your Institution's respective use, handling or storage of the SOFTWARE.
> # If publications result from research using this SOFTWARE, we ask that the Ontario Institute for Cancer Research be acknowledged and/or
> # credit be given to OICR scientists, as scientifically appropriate.
> 
> Sys.setenv("R_TESTS" = "")
> 
> library('testthat')
> library('bedr')


######################
#### bedr v1.1.3 ####
######################

checking binary availability...
  * Checking path for bedtools... FAIL
  * Checking path for bedops... FAIL
  * Checking path for tabix... FAIL
tests and examples will be skipped on R CMD check if binaries are missing

> 
> test_check('bedr')
  * Checking path for bedtools... FAIL
  * Checking path for tabix... FAIL
  * Checking path for bedtools... FAIL
  * Checking path for bedtools... FAIL
  * Checking path for bedtools... FAIL
  * Checking path for bedtools... FAIL
  * Checking path for bedtools... FAIL
  * Checking path for bedtools... FAIL
  * Checking path for bedtools... FAIL
  * Checking path for tabix... FAIL
READING VCF
 * checking if file exists... PASS
 * Reading vcf header...
   Done
 * Reading vcf body...
   Done
 * Parse vcf header...
   Done
 * Split info...
 * Done
CONVERT VCF TO BEDPE
PROCESSING BND BREAKENDS
CONVERT VCF TO BEDPE
PROCESSING BND BREAKENDS
CONVERT VCF TO BEDPE
 * This is not an vcf!
CONVERT VCF TO BEDPE
READING VCF
 * checking if file exists... PASS
 * Reading vcf header...
   Done
 * Reading vcf body...
   Done
 * Parse vcf header...
   Done
 * Split info...
 * Done
CONVERT VCF TO BEDPE
PROCESSING SIMPLE BREAKENDS
PROCESSING BND BREAKENDS
CONVERT VCF TO BEDPE
 * This is not an vcf!
CONVERT VCF TO BEDPE
READING VCF
 * checking if file exists... PASS
 * Reading vcf header...
   Done
 * Reading vcf body...
   Done
 * Parse vcf header...
   Done
 * Split info...
 * Done
CONVERT VCF TO BEDPE
PROCESSING SIMPLE BREAKENDS
PROCESSING BND BREAKENDS
CONVERT VCF TO BEDPE
 * This is not an vcf!
CONVERT VCF TO BEDPE
[ FAIL 0 | WARN 0 | SKIP 10 | PASS 18 ]

══ Skipped tests (10) ══════════════════════════════════════════════════════════
• empty test (10): 'test-convert2bed.R:13:1', 'test-determine.input.R:13:1',
  'test-in.region.R:13:1', 'test-is.merged.region.R:12:1',
  'test-is.sorted.region.R:13:1', 'test-process.input.R:13:1',
  'test-sort.region.R:15:1', 'test-sort.region.R:46:1',
  'test-sort.region.R:63:1', 'test-tabix.R:13:1'

[ FAIL 0 | WARN 0 | SKIP 10 | PASS 18 ]
> 
> proc.time()
   user  system elapsed 
   2.67    0.40    5.09