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### Running command:
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###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:sccomp.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings sccomp_1.3.5.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/sccomp.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 10.4.0
    GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'sccomp/DESCRIPTION' ... OK
* this is package 'sccomp' version '1.3.5'
* 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 whether package 'sccomp' can be installed ... OK
* used C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
* checking installed package size ... NOTE
  installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   3.6Mb
* 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 R 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
alpha_to_CI: no visible binding for global variable 'M'
alpha_to_CI: no visible binding for global variable 'C_name'
alpha_to_CI: no visible binding for global variable '.lower'
alpha_to_CI: no visible binding for global variable '.median'
alpha_to_CI: no visible binding for global variable '.upper'
as_matrix: no visible binding for global variable 'variable'
beta_to_CI: no visible binding for global variable 'M'
beta_to_CI: no visible binding for global variable 'C_name'
beta_to_CI: no visible binding for global variable '.lower'
beta_to_CI: no visible binding for global variable '.median'
beta_to_CI: no visible binding for global variable '.upper'
check_if_within_posterior: no visible binding for global variable
  '.lower'
check_if_within_posterior: no visible binding for global variable
  '.upper'
check_if_within_posterior: no visible binding for global variable 'ppc'
check_random_intercept_design: no visible binding for global variable
  'factors'
check_random_intercept_design: no visible binding for global variable
  'groupings'
contrasts_to_enquos: no visible binding for global variable '.'
data_simulation_to_model_input: no visible binding for global variable
  '.'
data_spread_to_model_input: no visible global function definition for
  'as.formula'
data_spread_to_model_input: no visible binding for global variable
  'exposure'
data_spread_to_model_input: no visible binding for global variable
  'design'
data_spread_to_model_input: no visible binding for global variable
  'mat'
data_spread_to_model_input: no visible binding for global variable
  'is_factor_continuous'
data_spread_to_model_input: no visible binding for global variable
  'design_matrix'
data_spread_to_model_input: no visible binding for global variable '.'
data_spread_to_model_input: no visible binding for global variable
  'minus_sum'
data_spread_to_model_input: no visible binding for global variable
  'mean_idx'
data_spread_to_model_input: no visible binding for global variable
  'group___numeric'
data_spread_to_model_input: no visible binding for global variable
  'idx'
data_spread_to_model_input: no visible binding for global variable
  'group___label'
data_spread_to_model_input: no visible binding for global variable
  'parameter'
data_spread_to_model_input: no visible binding for global variable
  'design_matrix_col'
data_to_spread: no visible binding for global variable 'exposure'
design_matrix_and_coefficients_to_dir_mult_simulation: no visible
  binding for global variable 'cell_type'
design_matrix_and_coefficients_to_dir_mult_simulation: no visible
  binding for global variable 'generated_counts'
design_matrix_and_coefficients_to_dir_mult_simulation: no visible
  binding for global variable 'factor_1'
design_matrix_and_coefficients_to_simulation: no visible binding for
  global variable 'cell_type'
design_matrix_and_coefficients_to_simulation: no visible binding for
  global variable 'beta_1'
design_matrix_and_coefficients_to_simulation: no visible binding for
  global variable 'beta_2'
dirichlet_multinomial_glm: no visible global function definition for
  'detect_cores'
dirichlet_multinomial_glm: no visible binding for global variable
  'glm_dirichlet_multinomial'
dirichlet_multinomial_glm: no visible binding for global variable
  'censoring_iteration'
dirichlet_multinomial_glm: no visible binding for global variable '.'
dirichlet_multinomial_glm: no visible binding for global variable
  'chains'
dirichlet_multinomial_glm: no visible binding for global variable
  'precision'
dirichlet_multinomial_glm: no visible binding for global variable 'M'
do_inference_imputation: no visible binding for global variable
  'glm_dirichlet_multinomial_imputation'
draws_to_statistics: no visible binding for global variable 'M'
draws_to_statistics: no visible binding for global variable 'parameter'
draws_to_statistics: no visible binding for global variable
  'bigger_zero'
draws_to_statistics: no visible binding for global variable
  'smaller_zero'
draws_to_statistics: no visible binding for global variable 'lower'
draws_to_statistics: no visible binding for global variable 'effect'
draws_to_statistics: no visible binding for global variable 'upper'
draws_to_statistics: no visible binding for global variable 'pH0'
draws_to_statistics: no visible binding for global variable 'FDR'
draws_to_statistics: no visible binding for global variable 'n_eff'
draws_to_statistics: no visible binding for global variable 'R_k_hat'
draws_to_tibble_x: no visible binding for global variable '.'
draws_to_tibble_x: no visible binding for global variable 'dummy'
draws_to_tibble_x: no visible binding for global variable '.variable'
draws_to_tibble_x: no visible binding for global variable '.chain'
draws_to_tibble_x: no visible binding for global variable '.iteration'
draws_to_tibble_x: no visible binding for global variable '.draw'
draws_to_tibble_x: no visible binding for global variable '.value'
draws_to_tibble_x_y: no visible binding for global variable '.'
draws_to_tibble_x_y: no visible binding for global variable 'dummy'
draws_to_tibble_x_y: no visible binding for global variable '.variable'
draws_to_tibble_x_y: no visible binding for global variable '.chain'
draws_to_tibble_x_y: no visible binding for global variable
  '.iteration'
draws_to_tibble_x_y: no visible binding for global variable '.draw'
draws_to_tibble_x_y: no visible binding for global variable '.value'
estimate_multi_beta_binomial_glm: no visible binding for global
  variable 'N'
estimate_multi_beta_binomial_glm: no visible binding for global
  variable 'M'
estimate_multi_beta_binomial_glm: no visible binding for global
  variable '5%'
estimate_multi_beta_binomial_glm: no visible binding for global
  variable '95%'
estimate_multi_beta_binomial_glm: no visible binding for global
  variable 'truncation_up'
estimate_multi_beta_binomial_glm: no visible binding for global
  variable 'truncation_down'
estimate_multi_beta_binomial_glm: no visible binding for global
  variable '.lower'
estimate_multi_beta_binomial_glm: no visible binding for global
  variable '.'
estimate_multi_beta_binomial_glm: no visible binding for global
  variable '50%'
estimate_multi_beta_binomial_glm: no visible binding for global
  variable '.upper'
find_optimal_number_of_chains: no visible binding for global variable
  'chains'
find_optimal_number_of_chains: no visible binding for global variable
  '.'
fit_and_generate_quantities: no visible binding for global variable 'N'
fit_and_generate_quantities: no visible binding for global variable 'M'
fit_and_generate_quantities: no visible binding for global variable
  'precision'
fit_model: no visible binding for global variable '.'
fit_model_and_parse_out_missing_data: no visible binding for global
  variable 'N'
fit_model_and_parse_out_missing_data: no visible binding for global
  variable 'M'
fit_model_and_parse_out_missing_data: no visible binding for global
  variable 'cores'
fit_model_and_parse_out_missing_data: no visible binding for global
  variable 'additional_parameters_to_save'
fit_model_and_parse_out_missing_data: no visible binding for global
  variable 'pass_fit'
fit_model_and_parse_out_missing_data: no visible binding for global
  variable 'tol_rel_obj'
fit_model_and_parse_out_missing_data: no visible binding for global
  variable 'glm_dirichlet_multinomial_generate_quantities'
fit_model_and_parse_out_missing_data: no visible binding for global
  variable '.draw'
fit_model_and_parse_out_missing_data: no visible binding for global
  variable '.chain'
fit_model_and_parse_out_missing_data: no visible binding for global
  variable '.iteration'
fit_model_and_parse_out_missing_data: no visible binding for global
  variable '.draw_imputation'
fit_model_and_parse_out_missing_data: no visible binding for global
  variable '.variable'
fit_model_and_parse_out_missing_data: no visible binding for global
  variable 'fit_list'
fit_model_and_parse_out_missing_data: no visible binding for global
  variable 'n_eff'
fit_model_and_parse_out_missing_data: no visible binding for global
  variable 'se_mean'
fit_model_and_parse_out_missing_data: no visible binding for global
  variable 'sd'
fit_model_and_parse_out_missing_data: no visible binding for global
  variable '.'
fit_model_and_parse_out_missing_data: no visible binding for global
  variable 'C_name'
fit_model_and_parse_out_missing_data: no visible binding for global
  variable '.lower'
fit_model_and_parse_out_missing_data: no visible binding for global
  variable '.median'
fit_model_and_parse_out_missing_data: no visible binding for global
  variable '.upper'
fit_model_and_parse_out_missing_data: no visible binding for global
  variable '5%'
fit_model_and_parse_out_missing_data: no visible binding for global
  variable '95%'
fit_model_and_parse_out_missing_data: no visible binding for global
  variable '50%'
fit_model_and_parse_out_missing_data: no visible binding for global
  variable 'precision'
fit_model_and_parse_out_no_missing_data: no visible binding for global
  variable 'glm_dirichlet_multinomial_generate_quantities'
fit_to_counts_rng: no visible binding for global variable '.variable'
fit_to_counts_rng: no visible binding for global variable 'S'
fit_to_counts_rng: no visible binding for global variable 'G'
fit_to_counts_rng: no visible binding for global variable '.'
generate_quantities: no visible binding for global variable 'N_M'
generate_quantities: no visible binding for global variable
  'generated_quantity'
generate_quantities: no visible binding for global variable 'draw'
generate_quantities: no visible binding for global variable 'N'
generate_quantities: no visible binding for global variable 'M'
get_FDR: no visible binding for global variable 'value'
get_FDR: no visible binding for global variable 'name'
get_FDR: no visible binding for global variable 'FDR'
get_abundance_contrast_draws: no visible binding for global variable
  'X'
get_abundance_contrast_draws: no visible binding for global variable
  '.value'
get_abundance_contrast_draws: no visible binding for global variable
  '.'
get_abundance_contrast_draws: no visible binding for global variable
  'X_random_intercept'
get_abundance_contrast_draws: no visible binding for global variable
  '.variable'
get_abundance_contrast_draws: no visible binding for global variable
  'y'
get_abundance_contrast_draws: no visible binding for global variable
  'M'
get_abundance_contrast_draws: no visible binding for global variable
  'parameter'
get_abundance_contrast_draws: no visible binding for global variable
  'n_eff'
get_abundance_contrast_draws: no visible binding for global variable
  'R_k_hat'
get_design_matrix: no visible binding for global variable '.'
get_mean_precision: no visible binding for global variable 'M'
get_mean_precision: no visible binding for global variable '2.5%'
get_mean_precision: no visible binding for global variable '97.5%'
get_mean_precision_association: no visible binding for global variable
  '.'
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_OLD: no visible binding for global variable
  '.'
get_probability_non_zero_OLD: no visible binding for global variable
  '.draw'
get_probability_non_zero_OLD: no visible binding for global variable
  'M'
get_probability_non_zero_OLD: no visible binding for global variable
  'C_name'
get_probability_non_zero_OLD: no visible binding for global variable
  'bigger_zero'
get_probability_non_zero_OLD: no visible binding for global variable
  'smaller_zero'
get_random_intercept_design: no visible binding for global variable
  'is_factor_continuous'
get_random_intercept_design: no visible binding for global variable
  'design'
get_random_intercept_design: no visible binding for global variable
  'max_mean_idx'
get_random_intercept_design: no visible binding for global variable
  'max_minus_sum'
get_random_intercept_design: no visible binding for global variable
  'max_factor_numeric'
get_random_intercept_design: no visible binding for global variable
  'max_group_numeric'
get_random_intercept_design: no visible binding for global variable
  'min_mean_idx'
get_random_intercept_design: no visible binding for global variable
  'min_minus_sum'
get_variability_contrast_draws: no visible binding for global variable
  'XA'
get_variability_contrast_draws: no visible binding for global variable
  '.value'
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
  'y'
get_variability_contrast_draws: no visible binding for global variable
  'M'
get_variability_contrast_draws: no visible binding for global variable
  'parameter'
get_variability_contrast_draws: no visible binding for global variable
  'n_eff'
get_variability_contrast_draws: no visible binding for global variable
  'R_k_hat'
glm_multi_beta: no visible binding for global variable '.'
label_deleterious_outliers: no visible binding for global variable
  '.count'
label_deleterious_outliers: no visible binding for global variable
  '95%'
label_deleterious_outliers: no visible binding for global variable '5%'
label_deleterious_outliers: no visible binding for global variable 'X'
label_deleterious_outliers: no visible binding for global variable
  'iteration'
label_deleterious_outliers: no visible binding for global variable
  'outlier_above'
label_deleterious_outliers: no visible binding for global variable
  'slope'
label_deleterious_outliers: no visible binding for global variable
  'is_group_right'
label_deleterious_outliers: no visible binding for global variable
  'outlier_below'
multi_beta_glm: no visible global function definition for
  'detect_cores'
parse_fit: no visible binding for global variable 'M'
parse_formula: no visible global function definition for 'terms'
parse_formula: no visible binding for global variable '.'
parse_formula_random_intercept: no visible global function definition
  for 'terms'
parse_generated_quantities: no visible binding for global variable
  '.draw'
parse_generated_quantities: no visible binding for global variable 'N'
parse_generated_quantities: no visible binding for global variable
  '.value'
parse_generated_quantities: no visible binding for global variable
  'generated_counts'
parse_generated_quantities: no visible binding for global variable 'M'
parse_generated_quantities: no visible binding for global variable
  'generated_proportions'
plot_1d_intervals: no visible binding for global variable 'parameter'
plot_1d_intervals: no visible binding for global variable 'estimate'
plot_1d_intervals: no visible binding for global variable 'value'
plot_2d_intervals: no visible binding for global variable 'v_effect'
plot_2d_intervals: no visible binding for global variable 'parameter'
plot_2d_intervals: no visible binding for global variable '.'
plot_2d_intervals: no visible binding for global variable 'c_effect'
plot_2d_intervals: no visible binding for global variable 'c_lower'
plot_2d_intervals: no visible binding for global variable 'c_upper'
plot_2d_intervals: no visible binding for global variable 'c_FDR'
plot_2d_intervals: no visible binding for global variable 'v_lower'
plot_2d_intervals: no visible binding for global variable 'v_upper'
plot_2d_intervals: no visible binding for global variable 'v_FDR'
plot_2d_intervals: no visible binding for global variable
  'cell_type_label'
plot_boxplot: no visible binding for global variable 'stats_name'
plot_boxplot: no visible binding for global variable 'parameter'
plot_boxplot: no visible binding for global variable 'stats_value'
plot_boxplot: no visible binding for global variable 'count_data'
plot_boxplot: no visible binding for global variable
  'generated_proportions'
plot_boxplot: no visible binding for global variable 'proportion'
plot_boxplot: no visible binding for global variable 'name'
plot_boxplot: no visible binding for global variable 'outlier'
plot_summary: no visible binding for global variable 'parameter'
plot_summary: no visible binding for global variable 'count_data'
plot_summary: no visible binding for global variable 'v_effect'
remove_unwanted_variation.data.frame: no visible binding for global
  variable 'proportion_mean'
remove_unwanted_variation.data.frame: no visible binding for global
  variable 'y'
remove_unwanted_variation.data.frame: no visible binding for global
  variable 'observed_proportion'
remove_unwanted_variation.data.frame: no visible binding for global
  variable 'logit_residuals'
remove_unwanted_variation.data.frame: no visible binding for global
  variable 'exposure'
remove_unwanted_variation.data.frame: no visible binding for global
  variable 'adjusted_proportion'
remove_unwanted_variation.data.frame: no visible binding for global
  variable 'adjusted_counts'
replicate_data: no visible binding for global variable 'count_data'
replicate_data: no visible binding for global variable 'exposure'
replicate_data: no visible global function definition for 'tail'
replicate_data: no visible global function definition for 'as.formula'
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
  'is_factor_continuous'
replicate_data: no visible binding for global variable 'design_matrix'
replicate_data: no visible binding for global variable
  'X_random_intercept'
sccomp_predict.data.frame: no visible binding for global variable
  'count_data'
sccomp_predict.data.frame: no visible binding for global variable 'M'
sccomp_predict.data.frame: no visible binding for global variable 'N'
sccomp_predict.data.frame: no visible binding for global variable
  '2.5%'
sccomp_predict.data.frame: no visible binding for global variable
  '97.5%'
sccomp_replicate.data.frame: no visible binding for global variable 'N'
sccomp_replicate.data.frame: no visible binding for global variable 'M'
simulate_data.data.frame: no visible binding for global variable
  'data___'
simulate_data.data.frame: no visible binding for global variable
  '.exposure'
simulate_data.data.frame: no visible binding for global variable 'N'
simulate_data.data.frame: 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'
test_contrasts.data.frame: no visible binding for global variable
  'design_matrix_col'
test_contrasts.data.frame: no visible binding for global variable
  'parameter'
test_contrasts.data.frame: no visible binding for global variable 'M'
Undefined global functions or variables:
  . .chain .count .draw .draw_imputation .exposure .iteration .lower
  .median .upper .value .variable 2.5% 5% 50% 95% 97.5% C_name FDR G M
  N N_M R_k_hat S X XA X_random_intercept Xa
  additional_parameters_to_save adjusted_counts adjusted_proportion
  as.formula beta_1 beta_2 bigger_zero c_FDR c_effect c_lower c_upper
  cell_type cell_type_label censoring_iteration chains cores count_data
  data___ design design_matrix design_matrix_col detect_cores draw
  dummy effect estimate exposure factor_1 factors fit_list
  generated_counts generated_proportions generated_quantity
  glm_dirichlet_multinomial
  glm_dirichlet_multinomial_generate_quantities
  glm_dirichlet_multinomial_imputation group___label group___numeric
  groupings idx intercept_in_design is_factor_continuous is_group_right
  iteration logit_residuals lower mat max_factor_numeric
  max_group_numeric max_mean_idx max_minus_sum mean_idx min_mean_idx
  min_minus_sum minus_sum n_eff na.omit name observed_proportion
  outlier outlier_above outlier_below pH0 parameter pass_fit ppc
  precision proportion proportion_mean rnorm sd se_mean slope
  smaller_zero stats_name stats_value tail terms tol_rel_obj
  truncation_down truncation_up upper v_FDR v_effect v_lower v_upper
  value variable y
Consider adding
  importFrom("stats", "as.formula", "na.omit", "rnorm", "sd", "terms")
  importFrom("utils", "tail")
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 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'F:/biocbuild/bbs-3.17-bioc/R/library/sccomp/libs/x64/sccomp.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
test_contrasts            80.71   0.50   81.20
sccomp_glm                79.64   0.25   79.89
simulate_data             52.73   0.84   53.61
remove_unwanted_variation 45.33   1.30   46.66
plot_summary              39.72   1.13   40.86
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/sccomp.Rcheck/00check.log'
for details.