##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RCASPAR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RCASPAR_1.53.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/RCASPAR.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* 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 ‘RCASPAR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RCASPAR’ version ‘1.53.0’
* 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 ‘RCASPAR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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
kmplt_svrl: no visible global function definition for ‘lines’
kmplt_svrl: no visible global function definition for ‘legend’
logrnk: no visible global function definition for ‘pchisq’
pltprior: no visible global function definition for ‘persp’
weights_BLH: no visible global function definition for ‘optim’
Undefined global functions or variables:
  legend lines optim pchisq persp
Consider adding
  importFrom("graphics", "legend", "lines", "persp")
  importFrom("stats", "optim", "pchisq")
to your NAMESPACE file.
* checking Rd files ... NOTE
checkRd: (-1) STpredictor_BLH.Rd:21: Escaped LaTeX specials: \_
checkRd: (-1) STpredictor_BLH.Rd:39: Escaped LaTeX specials: \_
checkRd: (-1) STpredictor_BLH.Rd:78: Escaped LaTeX specials: \_
checkRd: (-1) STpredictor_BLH.Rd:79: Escaped LaTeX specials: \_ \_
checkRd: (-1) STpredictor_BLH.Rd:81: Escaped LaTeX specials: \_ \_
checkRd: (-1) STpredictor_BLH.Rd:82: Escaped LaTeX specials: \_
checkRd: (-1) deriv_weight_estimator_BLH.rd:41: Escaped LaTeX specials: \_
checkRd: (-1) deriv_weight_estimator_BLH.rd:45: Escaped LaTeX specials: \_
checkRd: (-1) deriv_weight_estimator_BLH.rd:46: Escaped LaTeX specials: \_
checkRd: (-1) deriv_weight_estimator_BLH.rd:64: Lost braces
    64 | \code{\link{weight_estimator_BLH}}, code{\link{deriv_weight_estimator_BLH_noprior}}
       |                                         ^
checkRd: (-1) deriv_weight_estimator_BLH_noprior.rd:17: Escaped LaTeX specials: \_
checkRd: (-1) deriv_weight_estimator_BLH_noprior.rd:36: Escaped LaTeX specials: \_
checkRd: (-1) deriv_weight_estimator_BLH_noprior.rd:40: Escaped LaTeX specials: \_
checkRd: (-1) deriv_weight_estimator_BLH_noprior.rd:41: Escaped LaTeX specials: \_
checkRd: (-1) logrnk.Rd:23: Escaped LaTeX specials: \_ \_
* 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 sizes of PDF files under ‘inst/doc’ ... 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/RCASPAR.Rcheck/00check.log’
for details.

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘RCASPAR’ ...
** 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 (RCASPAR)