##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:RCASPAR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings RCASPAR_1.52.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/RCASPAR.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘RCASPAR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RCASPAR’ version ‘1.52.0’
* 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 ‘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 loading without being on the library search path ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/RCASPAR.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL RCASPAR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-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)