##############################################################################
##############################################################################
###
### 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_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/scBFA.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 ‘scBFA/DESCRIPTION’ ... OK
* this is package ‘scBFA’ version ‘1.20.0’
* 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 ‘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
* 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-3.20-bioc/meat/scBFA.Rcheck/00check.log’
for details.