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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:sccomp.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings sccomp_2.1.16.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/sccomp.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 ‘sccomp/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sccomp’ version ‘2.1.16’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 21 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 ‘sccomp’ can be installed ... OK
* checking installed package size ... INFO
  installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data      3.9Mb
    figures   1.9Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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 ... NOTE
Namespaces in Imports field not imported from:
  ‘boot’ ‘cli’ ‘fansi’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
calculate_na_fraction_contribution : <anonymous> : <anonymous>: no
  visible binding for global variable ‘name’
calculate_na_fraction_contribution : <anonymous> : <anonymous>: no
  visible binding for global variable ‘fraction_contribution’
calculate_na_fraction_contribution : <anonymous>: no visible binding
  for global variable ‘factor_name’
calculate_na_fraction_contribution : <anonymous>: no visible binding
  for global variable ‘fraction_contribution’
check_and_install_cmdstanr : <anonymous>: no visible global function
  definition for ‘install.packages’
check_if_any_NA: no visible binding for global variable ‘columns’
check_if_columns_right_class: no visible global function definition for
  ‘is’
check_if_count_integer: no visible global function definition for ‘is’
check_if_sample_is_a_unique_identifier: no visible binding for global
  variable ‘n___’
check_sample_consistency_of_factors: no visible binding for global
  variable ‘name’
check_sample_consistency_of_factors: no visible binding for global
  variable ‘correct_size’
data_to_spread: no visible binding for global variable ‘exposure’
draws_to_statistics: no visible binding for global variable ‘rhat’
draws_to_statistics: no visible binding for global variable ‘ess_bulk’
draws_to_statistics: no visible binding for global variable ‘ess_tail’
draws_to_statistics: no visible binding for global variable ‘.value’
draws_to_statistics: no visible global function definition for
  ‘setNames’
draws_to_tibble_x_y: no visible binding for global variable ‘parameter’
find_optimal_number_of_chains: no visible binding for global variable
  ‘.’
fit_model: no visible global function definition for ‘setNames’
fit_model: no visible binding for global variable ‘pf’
get_abundance_contrast_draws: no visible global function definition for
  ‘setNames’
get_abundance_contrast_draws: no visible binding for global variable
  ‘.’
get_abundance_contrast_draws: no visible binding for global variable
  ‘parameters_name’
get_abundance_contrast_draws: no visible binding for global variable
  ‘n_random_eff’
get_abundance_contrast_draws: no visible binding for global variable
  ‘.chain’
get_abundance_contrast_draws: no visible binding for global variable
  ‘.iteration’
get_abundance_contrast_draws: no visible binding for global variable
  ‘.draw’
get_abundance_contrast_draws: no visible binding for global variable
  ‘X_random_effect_2’
get_model_from_data: no visible global function definition for
  ‘stan_model’
get_random_effect_design3: no visible binding for global variable
  ‘value’
get_random_effect_design3: no visible binding for global variable
  ‘group___label’
get_random_effect_design3: no visible binding for global variable
  ‘group___numeric’
get_variability_contrast_draws: no visible binding for global variable
  ‘parameters_name’
get_variability_contrast_draws: no visible binding for global variable
  ‘.variable’
get_variability_contrast_draws: no visible global function definition
  for ‘setNames’
get_variability_contrast_draws: no visible binding for global variable
  ‘.’
mutate_from_expr_list: no visible binding for global variable ‘M’
mutate_from_expr_list: no visible binding for global variable ‘.chain’
mutate_from_expr_list: no visible binding for global variable
  ‘.iteration’
mutate_from_expr_list: no visible binding for global variable ‘.draw’
parse_formula: no visible binding for global variable ‘.’
plot_2D_intervals: no visible binding for global variable ‘.’
plot_2D_intervals: no visible binding for global variable ‘c_pH0’
plot_2D_intervals: no visible binding for global variable ‘v_pH0’
plot_boxplot: no visible binding for global variable ‘factor_values’
plot_boxplot: no visible binding for global variable ‘is_zero’
plot_scatterplot: no visible binding for global variable
  ‘factor_values’
prepare_replicate_data: no visible global function definition for ‘is’
prepare_replicate_data: no visible binding for global variable
  ‘exposure’
prepare_replicate_data: no visible binding for global variable ‘dummy’
prepare_replicate_data: no visible global function definition for
  ‘tail’
prepare_replicate_data: no visible binding for global variable ‘.’
prepare_replicate_data: no visible global function definition for
  ‘na.omit’
prepare_replicate_data: no visible binding for global variable
  ‘formula’
prepare_replicate_data: no visible binding for global variable ‘design’
prepare_replicate_data: no visible binding for global variable
  ‘design_matrix’
print.sccomp_tbl: no visible binding for global variable ‘N’
print.sccomp_tbl: no visible binding for global variable ‘M’
print_red_tibble: no visible global function definition for
  ‘capture.output’
sccomp_boxplot: no visible binding for global variable ‘parameter’
sccomp_boxplot: no visible binding for global variable ‘proportion’
sccomp_boxplot: no visible binding for global variable
  ‘adjusted_proportion’
sccomp_calculate_residuals.sccomp_tbl: no visible binding for global
  variable ‘proportion_mean’
sccomp_calculate_residuals.sccomp_tbl: no visible binding for global
  variable ‘is_proportion’
sccomp_calculate_residuals.sccomp_tbl: no visible binding for global
  variable ‘y_proportion’
sccomp_calculate_residuals.sccomp_tbl: no visible binding for global
  variable ‘observed_proportion’
sccomp_calculate_residuals.sccomp_tbl: no visible binding for global
  variable ‘residuals’
sccomp_calculate_residuals.sccomp_tbl: no visible binding for global
  variable ‘exposure’
sccomp_glm_data_frame_counts: no visible global function definition for
  ‘is’
sccomp_glm_data_frame_counts: no visible global function definition for
  ‘gt’
sccomp_glm_data_frame_counts: no visible binding for global variable
  ‘N’
sccomp_glm_data_frame_counts: no visible binding for global variable
  ‘M’
sccomp_glm_data_frame_counts: no visible global function definition for
  ‘na.omit’
sccomp_predict.sccomp_tbl: no visible global function definition for
  ‘is’
sccomp_predict.sccomp_tbl: no visible binding for global variable ‘M’
sccomp_predict.sccomp_tbl: no visible binding for global variable ‘N’
sccomp_predict.sccomp_tbl: no visible binding for global variable
  ‘2.5%’
sccomp_predict.sccomp_tbl: no visible binding for global variable
  ‘97.5%’
sccomp_predict.sccomp_tbl: no visible binding for global variable
  ‘.value’
sccomp_predict.sccomp_tbl: no visible binding for global variable
  ‘.draw’
sccomp_proportional_fold_change.sccomp_tbl: no visible binding for
  global variable ‘ratio_mean’
sccomp_proportional_fold_change.sccomp_tbl: no visible binding for
  global variable ‘ratio_upper’
sccomp_proportional_fold_change.sccomp_tbl: no visible binding for
  global variable ‘proportion_fold_change’
sccomp_proportional_fold_change.sccomp_tbl: no visible binding for
  global variable ‘ratio_lower’
sccomp_proportional_fold_change.sccomp_tbl: no visible binding for
  global variable ‘difference_proportion_upper_fold_change’
sccomp_proportional_fold_change.sccomp_tbl: no visible binding for
  global variable ‘difference_proportion_lower_fold_change’
sccomp_proportional_fold_change.sccomp_tbl: no visible binding for
  global variable ‘average_uncertainty’
sccomp_proportional_fold_change.sccomp_tbl: no visible binding for
  global variable ‘statement’
sccomp_remove_outliers.sccomp_tbl: no visible global function
  definition for ‘is’
sccomp_remove_outliers.sccomp_tbl: no visible binding for global
  variable ‘N’
sccomp_remove_outliers.sccomp_tbl: no visible binding for global
  variable ‘M’
sccomp_remove_outliers.sccomp_tbl: no visible binding for global
  variable ‘5%’
sccomp_remove_outliers.sccomp_tbl: no visible binding for global
  variable ‘95%’
sccomp_remove_outliers.sccomp_tbl: no visible binding for global
  variable ‘truncation_up’
sccomp_remove_outliers.sccomp_tbl: no visible binding for global
  variable ‘truncation_down’
sccomp_remove_outliers.sccomp_tbl: no visible binding for global
  variable ‘value’
sccomp_remove_outliers.sccomp_tbl: no visible binding for global
  variable ‘columns’
sccomp_remove_outliers.sccomp_tbl: no visible binding for global
  variable ‘.lower’
sccomp_remove_outliers.sccomp_tbl: no visible binding for global
  variable ‘50%’
sccomp_remove_outliers.sccomp_tbl: no visible binding for global
  variable ‘.upper’
sccomp_remove_unwanted_effects.sccomp_tbl: no visible binding for
  global variable ‘proportion_mean’
sccomp_remove_unwanted_effects.sccomp_tbl: no visible binding for
  global variable ‘adjusted_proportion’
sccomp_remove_unwanted_effects.sccomp_tbl: no visible binding for
  global variable ‘exposure’
sccomp_remove_unwanted_effects.sccomp_tbl: no visible binding for
  global variable ‘adjusted_counts’
sccomp_replicate.sccomp_tbl: no visible binding for global variable ‘N’
sccomp_replicate.sccomp_tbl: no visible binding for global variable ‘M’
sccomp_test.sccomp_tbl: no visible binding for global variable
  ‘design_matrix_col’
sccomp_test.sccomp_tbl: no visible binding for global variable
  ‘parameter’
sccomp_test.sccomp_tbl: no visible binding for global variable ‘M’
simulate_data.tbl: no visible binding for global variable ‘data___’
simulate_data.tbl: no visible binding for global variable ‘.exposure’
simulate_data.tbl: no visible binding for global variable ‘N’
simulate_data.tbl: no visible binding for global variable ‘M’
summary_to_tibble: no visible binding for global variable ‘variable’
summary_to_tibble: no visible binding for global variable ‘.variable’
vb_iterative : <anonymous>: no visible binding for global variable
  ‘model_name’
Undefined global functions or variables:
  . .chain .draw .exposure .iteration .lower .upper .value .variable
  2.5% 5% 50% 95% 97.5% M N X_random_effect_2 adjusted_counts
  adjusted_proportion average_uncertainty c_pH0 capture.output columns
  correct_size data___ design design_matrix design_matrix_col
  difference_proportion_lower_fold_change
  difference_proportion_upper_fold_change dummy ess_bulk ess_tail
  exposure factor_name factor_values formula fraction_contribution
  group___label group___numeric gt install.packages is is_proportion
  is_zero model_name n___ n_random_eff na.omit name observed_proportion
  parameter parameters_name pf proportion proportion_fold_change
  proportion_mean ratio_lower ratio_mean ratio_upper residuals rhat
  setNames stan_model statement tail truncation_down truncation_up
  v_pH0 value variable y_proportion
Consider adding
  importFrom("methods", "is")
  importFrom("stats", "formula", "na.omit", "pf", "residuals",
             "setNames")
  importFrom("utils", "capture.output", "install.packages", "tail")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... INFO
Package unavailable to check Rd xrefs: ‘cmdstanr’
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in shell scripts ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/sccomp.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL sccomp
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘sccomp’ ...
** this is package ‘sccomp’ version ‘2.1.16’
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (sccomp)

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.

> library(testthat)
> library(sccomp)
Loading required package: instantiate
> 
> test_check("sccomp")
Starting 2 test processes
[ FAIL 0 | WARN 0 | SKIP 60 | PASS 0 ]

══ Skipped tests (60) ══════════════════════════════════════════════════════════
• On CRAN (59): 'test-NA-design-matrix.R:4:3', 'test-NA-design-matrix.R:45:3',
  'test-NA-design-matrix.R:90:3', 'test-column-types.R:8:3',
  'test-column-types.R:68:3', 'test-column-types.R:117:3',
  'test-get_random_effect_design3.R:9:3',
  'test-get_random_effect_design3.R:28:3',
  'test-get_random_effect_design3.R:64:3',
  'test-get_random_effect_design3.R:88:3',
  'test-get_random_effect_design3.R:134:3',
  'test-get_random_effect_design3.R:172:3',
  'test-get_random_effect_design3.R:211:3', 'test-plot.R:46:4',
  'test-plot.R:58:4', 'test-plot.R:70:4', 'test-plot.R:98:4',
  'test-plot.R:126:4', 'test-plot.R:158:4', 'test-plot.R:188:4',
  'test-plot.R:203:4', 'test-plot.R:217:4', 'test-plot.R:241:4',
  'test-plot.R:273:4', 'test-replicate_data.R:7:3',
  'test-replicate_data.R:91:3', 'test-replicate_data.R:180:3',
  'test-replicate_data.R:275:3', 'test-replicate_data.R:386:3',
  'test-replicate_data.R:485:3', 'test-replicate_data.R:615:3',
  'test-replicate_data.R:792:3', 'test-replicate_data.R:894:3',
  'test-replicate_data.R:955:3', 'test-replicate_data.R:1059:3',
  'test-sccomp_.R:86:3', 'test-sccomp_.R:111:3', 'test-sccomp_.R:130:3',
  'test-sccomp_.R:207:3', 'test-sccomp_.R:221:3', 'test-sccomp_.R:268:3',
  'test-sccomp_.R:317:3', 'test-sccomp_.R:381:3', 'test-sccomp_.R:407:3',
  'test-sccomp_.R:420:3', 'test-sccomp_.R:448:3', 'test-sccomp_.R:504:3',
  'test-sccomp_.R:523:3', 'test-sccomp_.R:537:3', 'test-sccomp_.R:549:3',
  'test-sccomp_.R:565:3', 'test-sccomp_.R:642:3', 'test-sccomp_.R:661:3',
  'test-sccomp_.R:690:3', 'test-sccomp_.R:765:3', 'test-sccomp_.R:829:3',
  'test-sccomp_.R:871:3', 'test-sccomp_.R:887:3', 'test-sccomp_.R:997:3'
• cmdstanr not available (1): 'test-convergence-metrics.R:3:3'

[ FAIL 0 | WARN 0 | SKIP 60 | PASS 0 ]
> 
> proc.time()
   user  system elapsed 
 33.260   2.091  23.622