##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:TOP.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings TOP_1.3.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/TOP.Rcheck’
* using R Under development (unstable) (2024-03-18 r86148)
* using platform: x86_64-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 Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TOP/DESCRIPTION’ ... OK
* this is package ‘TOP’ version ‘1.3.0’
* 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 ‘TOP’ 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
Surv_TOP_CI: no visible binding for global variable ‘offset’
TOP_coefPlot: no visible binding for global variable ‘lambda.min’
TOP_coefPlot: no visible binding for global variable ‘Features’
TOP_lambdaPlot: no visible binding for global variable ‘variable’
TOP_lambdaPlot: no visible binding for global variable ‘value’
TOP_lambdaPlot: no visible binding for global variable ‘Feature’
TOP_model: no visible binding for global variable ‘value’
TOP_model: no visible binding for global variable ‘SampleGroup’
TOP_model: no visible binding for global variable ‘n’
TOP_model: no visible binding for global variable ‘freq’
TOP_model: no visible binding for global variable ‘sd’
TOP_survival: no visible binding for global variable ‘coef’
TOP_survival: no visible binding for global variable ‘value’
TOP_survival: no visible binding for global variable ‘freq’
TOP_survival: no visible binding for global variable ‘sd’
TOP_survival: no visible binding for global variable ‘.’
TOP_survival: no visible binding for global variable ‘SampleGroup’
TOP_survival: no visible binding for global variable ‘n’
TOP_survivalPrediction: no visible binding for global variable ‘offset’
coefNetworkPlot: no visible binding for global variable ‘Features’
coefNetworkPlot: no visible binding for global variable ‘lambda.min’
coefNetworkPlot: no visible binding for global variable ‘score’
colCoxTests_combine: no visible binding for global variable ‘coef’
extractAUC: no visible binding for global variable ‘variable’
extractAUC: no visible binding for global variable ‘value’
simplenetworkPlot: no visible binding for global variable ‘Features’
simplenetworkPlot: no visible binding for global variable ‘lambda.min’
simplenetworkPlot: no visible binding for global variable ‘coef_abs’
simplenetworkPlot: no visible binding for global variable ‘from’
simplenetworkPlot: no visible binding for global variable ‘to’
simplenetworkPlot: no visible binding for global variable ‘name’
Undefined global functions or variables:
  . Feature Features SampleGroup coef coef_abs freq from lambda.min n
  name offset score sd to value variable
Consider adding
  importFrom("stats", "coef", "offset", "sd")
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 data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/TOP.Rcheck/00check.log’
for details.

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘TOP’ ...
** using staged installation
** R
** data
** 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 (TOP)