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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RNAseqCovarImpute.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RNAseqCovarImpute_1.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/RNAseqCovarImpute.Rcheck’
* using R version 4.4.2 (2024-10-31)
* 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 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RNAseqCovarImpute/DESCRIPTION’ ... OK
* this is package ‘RNAseqCovarImpute’ version ‘1.4.0’
* 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 ‘RNAseqCovarImpute’ 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 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
combine_rubins: no visible binding for global variable ‘probe’
combine_rubins: no visible binding for global variable ‘i’
combine_rubins: no visible binding for global variable ‘coef_combined’
combine_rubins: no visible binding for global variable ‘rubins_t_bayes’
combine_rubins: no visible binding for global variable ‘combined_p’
combine_rubins: no visible binding for global variable
  ‘combined_p_bayes’
limmavoom_imputed_data_list_helper: no visible binding for global
  variable ‘i’
limmavoom_imputed_data_list_helper: no visible binding for global
  variable ‘lm_predictor’
limmavoom_imputed_data_pca: no visible binding for global variable
  ‘probe’
lowess_all_gene_bins: no visible binding for global variable ‘gene_bin’
lowess_all_gene_bins: no visible binding for global variable ‘i’
voom_master_lowess: no visible global function definition for ‘is’
voom_master_lowess: no visible global function definition for ‘new’
voom_master_lowess: no visible global function definition for ‘lowess’
voom_master_lowess: no visible global function definition for
  ‘approxfun’
voom_sx_sy: no visible global function definition for ‘is’
voom_sx_sy: no visible global function definition for ‘new’
Undefined global functions or variables:
  approxfun coef_combined combined_p combined_p_bayes gene_bin i is
  lm_predictor lowess new probe rubins_t_bayes
Consider adding
  importFrom("methods", "is", "new")
  importFrom("stats", "approxfun", "lowess")
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 ... NOTE
Documented arguments not in \usage in Rd file 'impute_gene_bin_helper.Rd':
  ‘DGE’ ‘param’

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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                              user system elapsed
limmavoom_imputed_data_pca  19.227  2.631  15.278
limmavoom_imputed_data_list 16.113  2.174   5.428
combine_rubins              13.021  1.325   5.649
get_gene_bin_intervals      12.246  1.414   4.701
impute_by_gene_bin           9.761  1.214   4.891
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/RNAseqCovarImpute.Rcheck/00check.log’
for details.