##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:bedbaser.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings bedbaser_1.1.3.tar.gz
###
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##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/bedbaser.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘bedbaser/DESCRIPTION’ ... OK
* this is package ‘bedbaser’ version ‘1.1.3’
* 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 ‘bedbaser’ 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 ... NOTE
.get_url: no visible binding for global variable ‘access_methods’
.get_url: no visible binding for global variable ‘access_url’
.get_url: no visible binding for global variable ‘name’
.get_url: no visible binding for global variable ‘access_id’
bb_list_bedsets: no visible binding for global variable ‘bed_ids’
bb_list_bedsets: no visible binding for global variable ‘id’
bb_list_bedsets: no visible binding for global variable ‘name’
bb_list_bedsets: no visible binding for global variable ‘md5sum’
bb_list_bedsets: no visible binding for global variable
  ‘submission_date’
bb_list_bedsets: no visible binding for global variable
  ‘last_update_date’
bb_list_bedsets: no visible binding for global variable ‘description’
bb_list_bedsets: no visible binding for global variable ‘author’
Undefined global functions or variables:
  access_id access_methods access_url author bed_ids description id
  last_update_date md5sum name submission_date
* 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
bb_to_granges     5.228  0.395   6.398
bb_to_grangeslist 5.232  0.192   6.315
* 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:
  downloaded 467 KB
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 50 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-utils.R:28:5'): .get_extra_cols returns a named vector ─────────
  Error in `.get_extra_cols(file_path, 4, 1)`: x + y == dim(t)[2] is not TRUE
  Backtrace:
      ▆
   1. └─bedbaser:::.get_extra_cols(file_path, 4, 1) at test-utils.R:28:5
   2.   └─base::stopifnot(x + y == dim(t)[2])
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 50 ]
  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, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/bedbaser.Rcheck/00check.log’
for details.

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL bedbaser
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘bedbaser’ ...
** this is package ‘bedbaser’ version ‘1.1.3’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for ‘tags’ from package ‘AnVIL’ in package ‘bedbaser’
** 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 (bedbaser)

R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
> 
> library(testthat)
> library(bedbaser)
> 
> test_check("bedbaser")
trying URL 'https://api.bedbase.org/v1/files/files/4/3/4392bf6d534dfbdc2e3446dba1315fca.bed.gz'
Content type 'binary/octet-stream' length 72 bytes
==================================================
downloaded 72 bytes


Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min


Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname


Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

trying URL 'https://api.bedbase.org/v1/files/files/5/1/5170911fb566b43fd4e3a758b72187fb.bed.gz'
Content type 'binary/octet-stream' length 2842772 bytes (2.7 MB)
==================================================
downloaded 2.7 MB

trying URL 'https://api.bedbase.org/v1/files/files/d/4/d47891adc8a7320e69bf7b6acafa2ac1.bed.gz'
Content type 'binary/octet-stream' length 31017 bytes (30 KB)
==================================================
downloaded 30 KB

trying URL 'https://api.bedbase.org/v1/files/files/3/b/3b60e289fc46bc8377356439c5f1eb0f.bed.gz'
Content type 'binary/octet-stream' length 3488958 bytes (3.3 MB)
==================================================
downloaded 3.3 MB


Attaching package: 'BSgenome.Hsapiens.UCSC.hg19'

The following object is masked from 'package:BSgenome.Hsapiens.UCSC.hg38':

    Hsapiens

trying URL 'https://api.bedbase.org/v1/files/files/b/b/bbad85f21962bb8d972444f7f9a3a932.bed.gz'
Content type 'binary/octet-stream' length 641053 bytes (626 KB)
==================================================
downloaded 626 KB

trying URL 'https://api.bedbase.org/v1/files/files/5/7/57b1cfa0709db93cdf91cc77c229b0c7.bed.gz'
Content type 'binary/octet-stream' length 158206 bytes (154 KB)
==================================================
downloaded 154 KB

trying URL 'https://api.bedbase.org/v1/files/files/0/6/0692dfe199d26353af23dcbf354a6548.bed.gz'
Content type 'binary/octet-stream' length 478938 bytes (467 KB)
==================================================
downloaded 467 KB

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 50 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-utils.R:28:5'): .get_extra_cols returns a named vector ─────────
Error in `.get_extra_cols(file_path, 4, 1)`: x + y == dim(t)[2] is not TRUE
Backtrace:
    ▆
 1. └─bedbaser:::.get_extra_cols(file_path, 4, 1) at test-utils.R:28:5
 2.   └─base::stopifnot(x + y == dim(t)[2])

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 50 ]
Error: Test failures
Execution halted