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### Running command:
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###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:ProteinGymR.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings ProteinGymR_1.3.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.22-data-experiment/meat/ProteinGymR.Rcheck’
* using R version 4.5.0 (2025-04-11)
* 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 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘ProteinGymR/DESCRIPTION’ ... OK
* this is package ‘ProteinGymR’ version ‘1.3.0’
* 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 ‘ProteinGymR’ 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 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
plot_structure: warning in getProtIDs(assay_name = assay_name): partial
  argument match of 'assay_name' to 'assay_names'
benchmark_models: no visible binding for global variable ‘model’
benchmark_models: no visible binding for global variable ‘.data’
dms_corr_plot: no visible binding for global variable ‘uID’
dms_corr_plot: no visible binding for global variable ‘.data’
filter_by_pos: no visible binding for global variable ‘pos’
pg_filter_am_table: no visible binding for global variable ‘.data’
pg_match_id: no visible binding for global variable ‘.data’
plot_dms_heatmap: no visible binding for global variable ‘.data’
plot_dms_heatmap: no visible binding for global variable ‘DMS_score’
plot_dms_heatmap: no visible binding for global variable ‘ref’
plot_structure: no visible binding for global variable ‘.data’
plot_structure: no visible binding for global variable ‘pos’
plot_structure: no visible binding for global variable ‘DMS_score’
plot_structure: no visible global function definition for
  ‘colorRampPalette’
plot_zeroshot_heatmap: no visible binding for global variable ‘.data’
plot_zeroshot_heatmap: no visible binding for global variable ‘mutant’
plot_zeroshot_heatmap: no visible binding for global variable ‘ref’
supervised_metrics: no visible binding for global variable ‘eh’
Undefined global functions or variables:
  .data DMS_score colorRampPalette eh model mutant pos ref uID
Consider adding
  importFrom("grDevices", "colorRampPalette")
to your NAMESPACE file.
* 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 ... WARNING
Undocumented arguments in Rd file 'plot_dms_heatmap.Rd'
  ‘color_scheme’ ‘...’

Undocumented arguments in Rd file 'plot_structure.Rd'
  ‘color_scheme’
Documented arguments not in \usage in Rd file 'plot_structure.Rd':
  ‘pdb_data’

Undocumented arguments in Rd file 'plot_zeroshot_heatmap.Rd'
  ‘model’ ‘color_scheme’ ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘ProteinGymR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_zeroshot_heatmap
> ### Title: Visualize Zero Shot Scores Along a Protein
> ### Aliases: plot_zeroshot_heatmap
> 
> ### ** Examples
> 
> 
> available_models()
 [1] "Site_Independent"           "EVmutation"                
 [3] "DeepSequence_single"        "DeepSequence_ensemble"     
 [5] "EVE_single"                 "EVE_ensemble"              
 [7] "Unirep"                     "Unirep_evotune"            
 [9] "MSA_Transformer_single"     "MSA_Transformer_ensemble"  
[11] "ESM1b"                      "ESM1v_single"              
[13] "ESM1v_ensemble"             "ESM2_8M"                   
[15] "ESM2_35M"                   "ESM2_150M"                 
[17] "ESM2_650M"                  "ESM2_3B"                   
[19] "ESM2_15B"                   "Wavenet"                   
[21] "RITA_s"                     "RITA_m"                    
[23] "RITA_l"                     "RITA_xl"                   
[25] "Progen2_small"              "Progen2_medium"            
[27] "Progen2_base"               "Progen2_large"             
[29] "Progen2_xlarge"             "GEMME"                     
[31] "VESPA"                      "VESPAl"                    
[33] "VespaG"                     "ProtGPT2"                  
[35] "Tranception_S_no_retrieval" "Tranception_M_no_retrieval"
[37] "Tranception_L_no_retrieval" "Tranception_S"             
[39] "Tranception_M"              "Tranception_L"             
[41] "TranceptEVE_S"              "TranceptEVE_M"             
[43] "TranceptEVE_L"              "CARP_38M"                  
[45] "CARP_600K"                  "CARP_640M"                 
[47] "CARP_76M"                   "MIF"                       
[49] "MIFST"                      "ESM_IF1"                   
[51] "ProteinMPNN"                "ProtSSN_k10_h512"          
[53] "ProtSSN_k10_h768"           "ProtSSN_k10_h1280"         
[55] "ProtSSN_k20_h512"           "ProtSSN_k20_h768"          
[57] "ProtSSN_k20_h1280"          "ProtSSN_k30_h512"          
[59] "ProtSSN_k30_h768"           "ProtSSN_k30_h1280"         
[61] "ProtSSN_ensemble"           "SaProt_650M_AF2"           
[63] "SaProt_35M_AF2"             "PoET"                      
[65] "MULAN_small"                "ProSST_20"                 
[67] "ProSST_128"                 "ProSST_512"                
[69] "ProSST_1024"                "ProSST_2048"               
[71] "ProSST_4096"                "ESCOTT"                    
[73] "VenusREM"                   "RSALOR"                    
[75] "S2F"                        "S2F_MSA"                   
[77] "S3F"                        "S3F_MSA"                   
[79] "SiteRM"                    
> 
> model_data <- zeroshot_substitutions()
see ?ProteinGymR and browseVignettes('ProteinGymR') for documentation
loading from cache
> 
> plot_zeroshot_heatmap(assay_name = "A0A192B1T2_9HIV1_Haddox_2018", 
+     model_data = model_data, 
+     model = "GEMME",
+     start_pos = 600,
+     end_pos = 700, 
+     color_scheme = "EVE")
>     
> plot_zeroshot_heatmap(assay_name = "SRC_HUMAN_Nguyen_2022",
+     model_data = model_data,
+     model = "CARP_38M")
'start_pos' not provided, using the first position in the protein.
'end_pos' not provided, using the last position in the protein.
>     
> plot_zeroshot_heatmap(assay_name = "A0A192B1T2_9HIV1_Haddox_2018", 
+     model_data = model_data, 
+     model = "EVmutations",
+     start_pos = 10, 
+     end_pos = 80, 
+     exact_coord = TRUE)
Error in `dplyr::select()`:
ℹ In argument: `all_of(model)`.
Caused by error in `all_of()`:
! Can't subset elements that don't exist.
✖ Element `EVmutations` doesn't exist.
Backtrace:
     ▆
  1. ├─ProteinGymR::plot_zeroshot_heatmap(...)
  2. │ ├─dplyr::select(assay_df, mutant, all_of(model))
  3. │ └─dplyr:::select.data.frame(assay_df, mutant, all_of(model))
  4. │   └─tidyselect::eval_select(expr(c(...)), data = .data, error_call = error_call)
  5. │     └─tidyselect:::eval_select_impl(...)
  6. │       ├─tidyselect:::with_subscript_errors(...)
  7. │       │ └─base::withCallingHandlers(...)
  8. │       └─tidyselect:::vars_select_eval(...)
  9. │         └─tidyselect:::walk_data_tree(expr, data_mask, context_mask)
 10. │           └─tidyselect:::eval_c(expr, data_mask, context_mask)
 11. │             └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
 12. │               └─tidyselect:::walk_data_tree(new, data_mask, context_mask)
 13. │                 └─tidyselect:::eval_context(expr, context_mask, call = error_call)
 14. │                   ├─tidyselect:::with_chained_errors(...)
 15. │                   │ └─base::withCallingHandlers(...)
 16. │                   └─rlang::eval_tidy(as_quosure(expr, env), context_mask)
 17. ├─tidyselect::all_of(model)
 18. │ └─tidyselect:::as_indices_impl(x, vars = vars, strict = TRUE)
 19. │   └─tidyselect:::chr_as_locations(x, vars, call = call, arg = arg)
 20. │     └─vctrs::vec_as_location(...)
 21. └─vctrs (local) `<fn>`()
 22.   └─vctrs:::stop_subscript_oob(...)
 23.     └─vctrs:::stop_subscript(...)
 24.       └─rlang::abort(...)
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
plot_dms_heatmap 46.136  0.928  48.120
plot_structure   33.860  1.471  36.829
ProteinGym_DMS   22.870  1.706  25.048
dms_corr_plot    17.837  0.753  20.543
benchmark_models  5.358  0.806   6.644
* 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 ('test-dms_corr_plot.R:63:5'): that assay_name is required when `mode = 'by_assay'` ──
  Error in `dms_corr_plot_devel(model_table = "GEMME", dms_table = "some_table", 
      mode = "by_assay")`: could not find function "dms_corr_plot_devel"
  Backtrace:
      ▆
   1. └─testthat::expect_error(...) at test-dms_corr_plot.R:63:5
   2.   └─testthat:::expect_condition_matching(...)
   3.     └─testthat:::quasi_capture(...)
   4.       ├─testthat (local) .capture(...)
   5.       │ └─base::withCallingHandlers(...)
   6.       └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
  
  [ FAIL 6 | WARN 0 | SKIP 0 | PASS 13 ]
  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, 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.22-data-experiment/meat/ProteinGymR.Rcheck/00check.log’
for details.