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### Running command:
###
###   /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_1.3.6.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-data-experiment/meat/ProteinGymR.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 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘ProteinGymR/DESCRIPTION’ ... OK
* this is package ‘ProteinGymR’ version ‘1.3.6’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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
benchmark_models: no visible binding for global variable ‘.data’
color_line: no visible global function definition for ‘qnorm’
color_line: no visible global function definition for ‘ecdf’
color_line: no visible binding for global variable ‘aggregate_score’
color_line: no visible binding for global variable ‘quant_score’
color_line: no visible binding for global variable ‘quant_clamped’
color_line: no visible binding for global variable ‘color_index’
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’
model_corr_plot: no visible binding for global variable ‘uID’
model_corr_plot: no visible binding for global variable ‘.data’
model_match_id: no visible binding for global variable ‘model_df1’
model_match_id: no visible binding for global variable ‘model_df2’
model_match_id: no visible binding for global variable ‘DMS_id.y’
model_match_id: no visible binding for global variable ‘DMS_id.x’
model_match_id: no visible binding for global variable ‘UniProt_id’
model_match_id: no visible binding for global variable ‘mutant’
pg_filter_am_table: no visible binding for global variable ‘.data’
pg_match_id: no visible binding for global variable ‘DMS_score.y’
pg_match_id: no visible binding for global variable ‘DMS_score.x’
pg_match_id: no visible binding for global variable ‘UniProt_id’
pg_match_id: no visible binding for global variable ‘mutant’
pg_match_id: no visible binding for global variable ‘DMS_score’
plot_dms_heatmap: no visible binding for global variable ‘.data’
plot_dms_heatmap: no visible binding for global variable ‘ref’
plot_structure: no visible binding for global variable ‘DMS_score’
plot_structure: no visible binding for global variable ‘.data’
plot_structure: no visible binding for global variable
  ‘aggregate_score’
plot_structure: no visible global function definition for ‘qnorm’
plot_structure: no visible global function definition for ‘ecdf’
plot_structure: no visible binding for global variable ‘quant_score’
plot_structure: no visible binding for global variable ‘quant_clamped’
plot_zeroshot_heatmap: no visible binding for global variable ‘.data’
Undefined global functions or variables:
  .data DMS_id.x DMS_id.y DMS_score DMS_score.x DMS_score.y UniProt_id
  aggregate_score color_index ecdf model_df1 model_df2 mutant pos qnorm
  quant_clamped quant_score ref uID
Consider adding
  importFrom("stats", "ecdf", "qnorm")
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 ... 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
plot_structure        79.902  8.164  90.124
model_corr_plot       76.138  6.407  84.711
supervised_scores     55.788  5.157  62.576
plot_zeroshot_heatmap 48.784  4.400  53.625
dms_corr_plot         49.145  3.935  54.821
plot_dms_heatmap      44.598  2.931  48.511
zeroshot_scores       23.077  2.059  25.881
ProteinGym_DMS        23.299  1.807  25.512
benchmark_models       5.017  0.919   6.365
am_scores              4.082  0.653   5.117
* 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 ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.22-data-experiment/meat/ProteinGymR.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL ProteinGymR
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘ProteinGymR’ ...
** this is package ‘ProteinGymR’ version ‘1.3.6’
** 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 (ProteinGymR)

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(ProteinGymR)
> 
> test_check("ProteinGymR")
see ?ProteinGymR and browseVignettes('ProteinGymR') for documentation
loading from cache
Using default AlphaMissense modelfrom `ProteinGymR::am_scores()`.
see ?ProteinGymR and browseVignettes('ProteinGymR') for documentation
loading from cache
1 invalid values were found (fake_id) and removed from the query.
Field 'accession_id' with no valid entries has been removed from query.
No fold_scheme specified, using contiguous scheme as default.
Loading semi-supervised model scores with contiguous folding scheme
see ?ProteinGymR and browseVignettes('ProteinGymR') for documentation
loading from cache
'dms_table' not provided, using default table from `ProteinGymR::dms_substitutions()`
see ?ProteinGymR and browseVignettes('ProteinGymR') for documentation
loading from cache
[1] "r = 0.66; Pval = 0"
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 20 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 20 ]
> 
> proc.time()
   user  system elapsed 
 52.540   2.875  59.364