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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:HuBMAPR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings HuBMAPR_1.0.3.tar.gz
###
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* using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/HuBMAPR.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘HuBMAPR/DESCRIPTION’ ... OK
* this is package ‘HuBMAPR’ version ‘1.0.3’
* 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 ‘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: donors
> ### Title: HuBMAP Donors
> ### Aliases: donors donors_default_columns donor_detail donor_derived
> ###   donor_metadata
> 
> ### ** Examples
> 
> donors()
Error in `mutate()`:
ℹ In argument: `Body mass index = as.numeric(.data$`Body mass index`)`.
Caused by error in `` .data$`Body mass index` ``:
! Column `Body mass index` not found in `.data`.
Backtrace:
     ▆
  1. ├─HuBMAPR::donors()
  2. │ └─HuBMAPR:::.donor_edit(tbl)
  3. │   ├─dplyr::select(...)
  4. │   ├─dplyr::mutate(...)
  5. │   └─dplyr:::mutate.data.frame(...)
  6. │     └─dplyr:::mutate_cols(.data, dplyr_quosures(...), by)
  7. │       ├─base::withCallingHandlers(...)
  8. │       └─dplyr:::mutate_col(dots[[i]], data, mask, new_columns)
  9. │         └─mask$eval_all_mutate(quo)
 10. │           └─dplyr (local) eval()
 11. ├─Body mass index
 12. ├─rlang:::`$.rlang_data_pronoun`(.data, `Body mass index`)
 13. │ └─rlang:::data_pronoun_get(...)
 14. └─rlang:::abort_data_pronoun(x, call = y)
 15.   └─rlang::abort(msg, "rlang_error_data_pronoun_not_found", call = call)
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:
  Error in `mutate(.unnest_mutate_relocate(.donor_matadata_modify(unnest_longer(select(tbl, 
      "hubmap_id", "uuid", "group_name", "last_modified_timestamp", 
      "data_value", "preferred_term", "grouping_concept_preferred_term", 
      "data_type"), c("data_value", "preferred_term", "grouping_concept_preferred_term", 
      "data_type")))), Age = as.numeric(.data$Age), `Body Mass Index` = as.numeric(.data$`Body Mass Index`), 
      `Body mass index` = as.numeric(.data$`Body mass index`), 
      `Body Mass Index` = case_when(!is.na(.data$`Body Mass Index`) ~ 
          .data$`Body Mass Index`, is.na(.data$`Body Mass Index`) & 
          is.na(.data$`Body mass index`) ~ NA_real_, TRUE ~ .data$`Body mass index`))`: i In argument: `Body mass index = as.numeric(.data$`Body mass index`)`.
  Caused by error in `` .data$`Body mass index` ``:
  ! Column `Body mass index` not found in `.data`.
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 95 ]
  Error: Test failures
  Execution halted
* 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 ‘hubmapr_vignettes.Rmd’ using rmarkdown
The magick package is required to crop "/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/HuBMAPR.Rcheck/vign_test/HuBMAPR/vignettes/hubmapr_vignettes_files/figure-html/plot-1.png" but not available.

Quitting from lines 199-229 [derived using left_join] (hubmapr_vignettes.Rmd)
Error: processing vignette 'hubmapr_vignettes.Rmd' failed with diagnostics:
ℹ In argument: `Body mass index = as.numeric(.data$`Body mass index`)`.
Caused by error in `` .data$`Body mass index` ``:
! Column `Body mass index` not found in `.data`.
--- failed re-building ‘hubmapr_vignettes.Rmd’

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

Error: Vignette re-building failed.
Execution halted

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

Status: 3 ERRORs
See
  ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/HuBMAPR.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL HuBMAPR
###
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* installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘HuBMAPR’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** 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 (HuBMAPR)

R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 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 1 | WARN 0 | SKIP 0 | PASS 95 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_donors.R:2:3'): 'donors()' works ───────────────────────────────
<dplyr:::mutate_error/rlang_error/error/condition>
Error in `mutate(.unnest_mutate_relocate(.donor_matadata_modify(unnest_longer(select(tbl, 
    "hubmap_id", "uuid", "group_name", "last_modified_timestamp", 
    "data_value", "preferred_term", "grouping_concept_preferred_term", 
    "data_type"), c("data_value", "preferred_term", "grouping_concept_preferred_term", 
    "data_type")))), Age = as.numeric(.data$Age), `Body Mass Index` = as.numeric(.data$`Body Mass Index`), 
    `Body mass index` = as.numeric(.data$`Body mass index`), 
    `Body Mass Index` = case_when(!is.na(.data$`Body Mass Index`) ~ 
        .data$`Body Mass Index`, is.na(.data$`Body Mass Index`) & 
        is.na(.data$`Body mass index`) ~ NA_real_, TRUE ~ .data$`Body mass index`))`: i In argument: `Body mass index = as.numeric(.data$`Body mass index`)`.
Caused by error in `` .data$`Body mass index` ``:
! Column `Body mass index` not found in `.data`.

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 95 ]
Error: Test failures
Execution halted