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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:rigvf.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings rigvf_1.3.6.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/rigvf.Rcheck’
* using R version 4.6.0 alpha (2026-04-05 r89794)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-04-15 07:35:12 UTC
* checking for file ‘rigvf/DESCRIPTION’ ... OK
* this is package ‘rigvf’ version ‘1.3.6’
* 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 ‘rigvf’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* 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 loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... 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 ‘rigvf-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: catalog_queries
> ### Title: Query the IGVF Catalog via REST API
> ### Aliases: catalog_queries gene_variants variant_genes gene_elements
> ###   elements element_genes
> 
> ### ** Examples
> 
> 
> rigvf::gene_variants(gene_name = "GCK")
# A tibble: 25 × 18
   gene          sequence_variant effect_size log10pvalue posterior_inclusion_…¹
   <chr>         <chr>                  <dbl>       <dbl>                  <dbl>
 1 genes/ENSG00… variants/NC_000…      -1.01         9.06                 0.0599
 2 genes/ENSG00… variants/NC_000…      -0.347        7.93                 0.200 
 3 genes/ENSG00… variants/NC_000…      -0.565        6.93                 0.103 
 4 genes/ENSG00… variants/NC_000…       0.378        8.22                 0.0720
 5 genes/ENSG00… variants/NC_000…      -0.319        6.92                 0.0422
 6 genes/ENSG00… variants/NC_000…       0.349        7.54                 0.0170
 7 genes/ENSG00… variants/NC_000…      -1.02         9.39                 0.144 
 8 genes/ENSG00… variants/NC_000…      -0.340       10.2                  0.0234
 9 genes/ENSG00… variants/NC_000…      -0.486        7.03                 0.0129
10 genes/ENSG00… variants/NC_000…       0.262        4.45                 0.138 
# ℹ 15 more rows
# ℹ abbreviated name: ¹​posterior_inclusion_probability
# ℹ 13 more variables: standard_error <dbl>, z_score <dbl>,
#   credible_set_min_r2 <dbl>, method <chr>, source <chr>, source_url <chr>,
#   label <chr>, p_value <dbl>, biological_context <chr>, biosample_term <chr>,
#   study <chr>, name <chr>, class <chr>
> 
> rigvf::gene_variants(gene_name = "GCK", effect_size="gt:0.5")
# A tibble: 0 × 0
> 
> rigvf::gene_variants(gene_name = "GCK", verbose = TRUE)
# A tibble: 25 × 18
   gene         sequence_variant  effect_size log10pvalue posterior_inclusion_…¹
   <list>       <list>                  <dbl>       <dbl>                  <dbl>
 1 <named list> <named list [16]>      -1.01         9.06                 0.0599
 2 <named list> <named list [16]>      -0.347        7.93                 0.200 
 3 <named list> <named list [16]>      -0.565        6.93                 0.103 
 4 <named list> <named list [16]>       0.378        8.22                 0.0720
 5 <named list> <named list [16]>      -0.319        6.92                 0.0422
 6 <named list> <named list [16]>       0.349        7.54                 0.0170
 7 <named list> <named list [16]>      -1.02         9.39                 0.144 
 8 <named list> <named list [16]>      -0.340       10.2                  0.0234
 9 <named list> <named list [16]>      -0.486        7.03                 0.0129
10 <named list> <named list [16]>       0.262        4.45                 0.138 
# ℹ 15 more rows
# ℹ abbreviated name: ¹​posterior_inclusion_probability
# ℹ 13 more variables: standard_error <dbl>, z_score <dbl>,
#   credible_set_min_r2 <dbl>, method <chr>, source <chr>, source_url <chr>,
#   label <chr>, p_value <dbl>, biological_context <chr>, biosample_term <chr>,
#   study <list>, name <chr>, class <chr>
> 
> rigvf::variant_genes(spdi = "NC_000001.11:920568:G:A")
# A tibble: 0 × 0
> 
> res <- rigvf::gene_elements(gene_id = "ENSG00000187961")
> res
# A tibble: 25 × 13
   name   label method class source source_url biological_context biosample_term
   <chr>  <chr> <chr>  <chr> <chr>  <chr>      <chr>              <chr>         
 1 expre… regu… Pertu… obse… IGVF   https://d… CD8-positive, alp… ontology_term…
 2 expre… regu… Pertu… obse… IGVF   https://d… CD8-positive, alp… ontology_term…
 3 expre… regu… Pertu… obse… IGVF   https://d… CD8-positive, alp… ontology_term…
 4 expre… regu… Pertu… obse… IGVF   https://d… CD8-positive, alp… ontology_term…
 5 expre… regu… Pertu… obse… IGVF   https://d… CD8-positive, alp… ontology_term…
 6 expre… regu… Pertu… obse… IGVF   https://d… CD8-positive, alp… ontology_term…
 7 expre… regu… Pertu… obse… IGVF   https://d… CD8-positive, alp… ontology_term…
 8 expre… regu… Pertu… obse… IGVF   https://d… CD8-positive, alp… ontology_term…
 9 expre… regu… Pertu… obse… IGVF   https://d… CD8-positive, alp… ontology_term…
10 expre… regu… Pertu… obse… IGVF   https://d… CD8-positive, alp… ontology_term…
# ℹ 15 more rows
# ℹ 5 more variables: files_filesets <chr>, score <dbl>, p_value <int>,
#   genomic_element <chr>, gene <chr>
> res |>
+     tidyr::unnest_longer(elements) |>
+     tidyr::unnest_wider(elements)
Error in `tidyr::unnest_longer()`:
! Can't select columns that don't exist.
✖ Column `elements` doesn't exist.
Backtrace:
     ▆
  1. ├─tidyr::unnest_wider(tidyr::unnest_longer(res, elements), elements)
  2. │ └─tidyr:::check_data_frame(data)
  3. │   └─base::is.data.frame(x)
  4. ├─tidyr::unnest_longer(res, elements)
  5. │ └─tidyselect::eval_select(enquo(col), data, allow_rename = FALSE)
  6. │   └─tidyselect:::eval_select_impl(...)
  7. │     ├─tidyselect:::with_subscript_errors(...)
  8. │     │ └─base::withCallingHandlers(...)
  9. │     └─tidyselect:::vars_select_eval(...)
 10. │       └─tidyselect:::walk_data_tree(expr, data_mask, context_mask)
 11. │         └─tidyselect:::as_indices_sel_impl(...)
 12. │           └─tidyselect:::as_indices_impl(...)
 13. │             └─tidyselect:::chr_as_locations(x, vars, call = call, arg = arg)
 14. │               └─vctrs::vec_as_location(...)
 15. └─vctrs (local) `<fn>`() at vctrs/R/subscript-loc.R:84:3
 16.   └─vctrs:::stop_subscript_oob(...)
 17.     └─vctrs:::stop_subscript(...) at vctrs/R/subscript-loc.R:503:3
 18.       └─rlang::abort(...) at vctrs/R/subscript.R:150:3
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘rigvf.Rmd’ using rmarkdown

Quitting from rigvf.Rmd:101-108 [unnamed-chunk-5]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/vctrs_error_subscript_oob>
Error in `tidyr::unnest_longer()`:
! Can't select columns that don't exist.
✖ Column `elements` doesn't exist.
---
Backtrace:
    ▆
 1. ├─tidyr::unnest_wider(tidyr::unnest_longer(res, elements), elements)
 2. │ └─tidyr:::check_data_frame(data)
 3. │   └─base::is.data.frame(x)
 4. └─tidyr::unnest_longer(res, elements)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'rigvf.Rmd' failed with diagnostics:
Can't select columns that don't exist.
✖ Column `elements` doesn't exist.
--- failed re-building ‘rigvf.Rmd’

SUMMARY: processing the following file failed:
  ‘rigvf.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/rigvf.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL rigvf
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘rigvf’ ...
** this is package ‘rigvf’ version ‘1.3.6’
** 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 (rigvf)

R version 4.6.0 alpha (2026-04-05 r89794)
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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(rigvf)
> 
> test_check("rigvf")
[ FAIL 0 | WARN 0 | SKIP 2 | PASS 15 ]

══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• On CRAN (2): 'test-catalog.R:2:5', 'test-rigvf.R:28:5'

[ FAIL 0 | WARN 0 | SKIP 2 | PASS 15 ]
> 
> proc.time()
   user  system elapsed 
  3.086   0.284   3.357