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### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:HuBMAPR.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings HuBMAPR_1.2.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/HuBMAPR.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘HuBMAPR/DESCRIPTION’ ... OK
* this is package ‘HuBMAPR’ version ‘1.2.2’
* 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 ‘HuBMAPR’ 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 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 ‘HuBMAPR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: publications
> ### Title: HuBMAP Samples
> ### Aliases: publications publications_default_columns publication_detail
> ###   publication_data publication_authors
> 
> ### ** Examples
> 
> publications()
# A tibble: 14 × 7
   uuid     hubmap_id last_modified_timest…¹ publication_date publication_status
   <chr>    <chr>     <chr>                  <chr>            <chr>             
 1 f53d60b… HBM536.H… 2025-10-06             2025-08-20       FALSE             
 2 213e89c… HBM545.W… 2025-09-22             2025-07-01       TRUE              
 3 a10041a… HBM923.V… 2025-06-10             2025-05-23       FALSE             
 4 64ca708… HBM827.D… 2025-05-21             2025-06-03       TRUE              
 5 fa99f1a… HBM326.T… 2025-03-12             2025-03-12       TRUE              
 6 2ced91f… HBM885.X… 2023-07-18             2024-09-27       TRUE              
 7 aea510e… HBM332.M… 2023-07-18             2022-10-24       TRUE              
 8 77ab358… HBM222.S… 2023-07-18             2023-07-20       TRUE              
 9 dd0e7ae… HBM599.D… 2023-07-18             2023-07-19       TRUE              
10 3c72736… HBM629.D… 2023-07-18             2023-07-19       TRUE              
11 e833896… HBM695.W… 2023-07-18             2023-07-19       TRUE              
12 0de8528… HBM473.R… 2023-07-18             2023-07-19       TRUE              
13 eb97581… HBM464.W… 2023-07-18             2023-07-19       TRUE              
14 72cbeb8… HBM222.Z… 2023-07-18             2023-07-19       TRUE              
# ℹ abbreviated name: ¹​last_modified_timestamp
# ℹ 2 more variables: publication_venue <chr>, title <chr>
> publications_default_columns()
# A tibble: 7 × 1
  columns                
  <chr>                  
1 uuid                   
2 hubmap_id              
3 title                  
4 publication_venue      
5 last_modified_timestamp
6 publication_date       
7 publication_status     
> 
> uuid <- "2ced91fd6d543e79af90313e52ada57d"
> publication_detail(uuid)
# A tibble: 1 × 38
  ancestor_ids ancestors   contacts   contains_human_genetic_sequ…¹ contributors
  <list>       <list>      <list>     <lgl>                         <list>      
1 <chr [12]>   <list [12]> <list [1]> FALSE                         <list [6]>  
# ℹ abbreviated name: ¹​contains_human_genetic_sequences
# ℹ 33 more variables: created_by_user_displayname <chr>,
#   created_by_user_email <chr>, created_timestamp <dbl>,
#   creation_action <chr>, data_access_level <chr>, data_types <list>,
#   dataset_type <chr>, descendant_ids <list>, descendants <list>,
#   description <chr>, display_subtype <chr>, donor <list>, entity_type <chr>,
#   group_name <chr>, group_uuid <chr>, hubmap_id <chr>, …
> uuid <- "3c7273660cdf9ab91a7901533b2cd9a5"
> publication_data(uuid)
Error in `mutate()`:
ℹ In argument: `dataset_type = ifelse(...)`.
Caused by error in `map_chr()`:
ℹ In index: 61.
Caused by error:
! Result must be length 1, not 0.
Backtrace:
     ▆
  1. ├─HuBMAPR::publication_data(uuid)
  2. │ ├─dplyr::mutate(...)
  3. │ └─dplyr:::mutate.data.frame(...)
  4. │   └─dplyr:::mutate_cols(.data, dplyr_quosures(...), by)
  5. │     ├─base::withCallingHandlers(...)
  6. │     └─dplyr:::mutate_col(dots[[i]], data, mask, new_columns)
  7. │       └─mask$eval_all_mutate(quo)
  8. │         └─dplyr (local) eval()
  9. ├─base::ifelse(...)
 10. ├─purrr::map_chr(.data$uuid, ~.uuid_category(.x))
 11. │ └─purrr:::map_("character", .x, .f, ..., .progress = .progress)
 12. │   ├─purrr:::with_indexed_errors(...)
 13. │   │ └─base::withCallingHandlers(...)
 14. │   └─purrr:::call_with_cleanup(...)
 15. └─base::.handleSimpleError(...)
 16.   └─purrr (local) h(simpleError(msg, call))
 17.     └─cli::cli_abort(...)
 18.       └─rlang::abort(...)
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
          user system elapsed
donors   7.249  0.183  24.386
datasets 2.236  0.091   5.363
* 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:
      -"rui_location"), everything()), dataset_type = ifelse(is.na(.data$dataset_type), 
      map_chr(.data$uuid, ~.uuid_category(.x)), .data$dataset_type))`: i In argument: `dataset_type = ifelse(...)`.
  Caused by error in `map_chr()`:
  i In index: 61.
  Caused by error:
  ! Result must be length 1, not 0.
  ── Failure ('test_utilities.R:51:3'): '.uuid_category()' works ─────────────────
  .uuid_category("2e7123dcf2e9092a42ac42e44c2d686b") (`actual`) not equal to "Dataset" (`expected`).
  
  `actual` is NULL
  `expected` is a character vector ('Dataset')
  
  [ FAIL 3 | WARN 2 | SKIP 0 | PASS 94 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/HuBMAPR.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL HuBMAPR
###
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* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘HuBMAPR’ ...
** this is package ‘HuBMAPR’ version ‘1.2.2’
** 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 (HuBMAPR)

R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 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(HuBMAPR)
> 
> test_check("HuBMAPR")
[ FAIL 3 | WARN 2 | SKIP 0 | PASS 94 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_datasets.R:45:3'): 'dataset_metadata()' works ────────────────
nrow(tbl) > 0L && all(c("Key", "Value") %in% names(tbl)) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
── Error ('test_publications.R:30:3'): 'publication_authors()', 'publication_information()' and 'publication_data()' work with specific uuid ──
<dplyr:::mutate_error/rlang_error/error/condition>
Error in `mutate(unnest(select(.query_match(uuid, "hits.hits[]._source.ancestors[]"), 
    -"rui_location"), everything()), dataset_type = ifelse(is.na(.data$dataset_type), 
    map_chr(.data$uuid, ~.uuid_category(.x)), .data$dataset_type))`: i In argument: `dataset_type = ifelse(...)`.
Caused by error in `map_chr()`:
i In index: 61.
Caused by error:
! Result must be length 1, not 0.
── Failure ('test_utilities.R:51:3'): '.uuid_category()' works ─────────────────
.uuid_category("2e7123dcf2e9092a42ac42e44c2d686b") (`actual`) not equal to "Dataset" (`expected`).

`actual` is NULL
`expected` is a character vector ('Dataset')

[ FAIL 3 | WARN 2 | SKIP 0 | PASS 94 ]
Error: Test failures
Execution halted