##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:scBFA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings scBFA_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/scBFA.Rcheck’
* using R version 4.5.0 RC (2025-04-04 r88126)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scBFA/DESCRIPTION’ ... OK
* this is package ‘scBFA’ version ‘1.22.0’
* 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 ‘scBFA’ 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
InitBinaryFA: no visible global function definition for ‘as’
diagnose: no visible binding for global variable ‘disperPlot’
diagnose: no visible binding for global variable ‘fitted_disper’
diagnose: no visible binding for global variable ‘dataset_selection’
diagnose: no visible binding for global variable ‘variance’
Undefined global functions or variables:
  as dataset_selection disperPlot fitted_disper variance
Consider adding
  importFrom("methods", "as")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... NOTE
checkRd: (-1) InitBinaryFA.Rd:24: Lost braces
    24 | {A,Z,V,U,\eqn{\beta},\eqn{\gamma},\eqn{\epsilon}}}
       | ^
checkRd: (-1) InitBinaryFA.Rd:67: Lost braces
    67 | {A,Z,V,U,\eqn{\beta},\eqn{\gamma},\eqn{\epsilon}}.
       | ^
checkRd: (-1) restore.Rd:17: Lost braces; missing escapes or markup?
    17 | {A,Z,U,V,beta,gamma,epsilon}
       | ^
checkRd: (-1) scNoiseSim.Rd:22: Lost braces; missing escapes or markup?
    22 | r is varied in the set {0.5,1,5} in our simulation(as outlined in our paper)}
       |                        ^
checkRd: (-1) scNoiseSim.Rd:27: Lost braces; missing escapes or markup?
    27 | and in the paper is selected from the set {0.1, 0.5, 1, 2, 3}}
       |                                           ^
checkRd: (-1) scNoiseSim.Rd:32: Lost braces; missing escapes or markup?
    32 | and and in the paper is selected from the set {0.1, 0.5, 1, 2, 3}}
       |                                               ^
checkRd: (-1) scNoiseSim.Rd:35: Lost braces; missing escapes or markup?
    35 | and in the paper is selected from the set {-2, -0.5, 1,2.5,4}}
       |                                           ^
* 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 'restore.Rd':
  ‘parameters:’ ‘modelEnv:’

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 LazyData ... 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
diagnose 4.932  0.106   5.058
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/scBFA.Rcheck/00check.log’
for details.

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘scBFA’ ...
** this is package ‘scBFA’ version ‘1.22.0’
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (scBFA)

R version 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-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(scBFA)
> 
> test_check("scBFA")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 2 ]
> 
> proc.time()
   user  system elapsed 
 16.875   1.231  18.199