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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:sccomp.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings sccomp_1.10.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/sccomp.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘sccomp/DESCRIPTION’ ... OK
* this is package ‘sccomp’ version ‘1.10.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ‘sccomp’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data      4.0Mb
    figures   1.5Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘stats’ ‘knitr’
A package should be listed in only one of these fields.
* 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 dependencies in R code ... WARNING
'loadNamespace' or 'requireNamespace' call not declared from: ‘cmdstanr’
Namespaces in Imports field not imported from:
  ‘SeuratObject’ ‘callr’ ‘digest’ ‘fs’ ‘withr’
  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
check_if_columns_right_class: no visible global function definition for
  ‘is’
check_if_count_integer: no visible global function definition for ‘is’
data_to_spread: no visible binding for global variable ‘exposure’
draws_to_tibble_x_y: no visible binding for global variable ‘.’
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 binding for global variable ‘pf’
get_abundance_contrast_draws: no visible binding for global variable
  ‘.’
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_abundance_contrast_draws: no visible binding for global variable
  ‘Rhat’
get_model_from_data: no visible global function definition for
  ‘stan_model’
get_probability_non_zero: no visible binding for global variable ‘M’
get_probability_non_zero: no visible binding for global variable
  ‘C_name’
get_probability_non_zero: no visible binding for global variable
  ‘bigger_zero’
get_probability_non_zero: no visible binding for global variable
  ‘smaller_zero’
get_probability_non_zero_: no visible binding for global variable
  ‘name’
get_probability_non_zero_: no visible binding for global variable
  ‘value’
get_probability_non_zero_OLD: no visible binding for global variable
  ‘.’
get_variability_contrast_draws: no visible binding for global variable
  ‘.’
get_variability_contrast_draws: no visible binding for global variable
  ‘.variable’
get_variability_contrast_draws: no visible binding for global variable
  ‘Rhat’
parse_formula: no visible binding for global variable ‘.’
plot_2D_intervals: no visible binding for global variable ‘.’
replicate_data: no visible binding for global variable ‘count_data’
replicate_data: no visible global function definition for ‘is’
replicate_data: no visible binding for global variable ‘exposure’
replicate_data: no visible binding for global variable ‘dummy’
replicate_data: no visible global function definition for ‘tail’
replicate_data: no visible binding for global variable ‘.’
replicate_data: no visible global function definition for ‘na.omit’
replicate_data: no visible binding for global variable ‘Xa’
replicate_data: no visible binding for global variable
  ‘intercept_in_design’
replicate_data: no visible binding for global variable ‘design’
replicate_data: no visible binding for global variable ‘design_matrix’
replicate_data: no visible binding for global variable
  ‘X_random_effect’
replicate_data: no visible binding for global variable
  ‘X_random_effect_2’
sccomp_boxplot: no visible binding for global variable ‘parameter’
sccomp_boxplot: no visible binding for global variable ‘count_data’
sccomp_boxplot: no visible binding for global variable
  ‘multipanel_theme’
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 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 binding for global variable
  ‘count_data’
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 binding for global
  variable ‘count_data’
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_variation.sccomp_tbl: no visible binding for
  global variable ‘proportion_mean’
sccomp_remove_unwanted_variation.sccomp_tbl: no visible binding for
  global variable ‘adjusted_proportion’
sccomp_remove_unwanted_variation.sccomp_tbl: no visible binding for
  global variable ‘exposure’
sccomp_remove_unwanted_variation.sccomp_tbl: no visible binding for
  global variable ‘adjusted_counts’
sccomp_replicate.sccomp_tbl: no visible binding for global variable
  ‘count_data’
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’
simulate_multinomial_logit_linear: no visible global function
  definition for ‘rnorm’
summary_to_tibble: no visible binding for global variable ‘.’
summary_to_tibble: no visible binding for global variable ‘variable’
Undefined global functions or variables:
  . .chain .draw .exposure .iteration .lower .upper .value .variable
  2.5% 5% 50% 95% 97.5% C_name M N Rhat X_random_effect
  X_random_effect_2 Xa adjusted_counts adjusted_proportion
  average_uncertainty bigger_zero columns count_data data___ design
  design_matrix design_matrix_col
  difference_proportion_lower_fold_change
  difference_proportion_upper_fold_change dummy exposure
  intercept_in_design is is_proportion multipanel_theme n_random_eff
  na.omit name observed_proportion parameter pf proportion_fold_change
  proportion_mean ratio_lower ratio_mean ratio_upper residuals rnorm
  smaller_zero stan_model statement tail truncation_down truncation_up
  value variable y_proportion
Consider adding
  importFrom("methods", "is")
  importFrom("stats", "na.omit", "pf", "residuals", "rnorm")
  importFrom("utils", "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 ... 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 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/sccomp.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL sccomp
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘sccomp’ ...
** 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 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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)
> 
> test_check("sccomp")
[ FAIL 0 | WARN 0 | SKIP 19 | PASS 0 ]

══ Skipped tests (19) ══════════════════════════════════════════════════════════
• On CRAN (19): 'test-sccomp_.R:93:3', 'test-sccomp_.R:112:3',
  'test-sccomp_.R:163:3', 'test-sccomp_.R:177:3', 'test-sccomp_.R:224:3',
  'test-sccomp_.R:265:3', 'test-sccomp_.R:329:3', 'test-sccomp_.R:355:3',
  'test-sccomp_.R:368:3', 'test-sccomp_.R:405:3', 'test-sccomp_.R:461:3',
  'test-sccomp_.R:480:3', 'test-sccomp_.R:494:3', 'test-sccomp_.R:506:3',
  'test-sccomp_.R:517:3', 'test-sccomp_.R:530:3', 'test-sccomp_.R:542:3',
  'test-sccomp_.R:589:3', 'test-sccomp_.R:620:3'

[ FAIL 0 | WARN 0 | SKIP 19 | PASS 0 ]
> 
> proc.time()
   user  system elapsed 
  3.033   0.123   3.155