##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:iterativeBMAsurv.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings iterativeBMAsurv_1.64.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/iterativeBMAsurv.Rcheck’
* using R version 4.4.2 (2024-10-31)
* 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 ‘iterativeBMAsurv/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘iterativeBMAsurv’ version ‘1.64.0’
* 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 ‘iterativeBMAsurv’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘survival’
A package should be listed in only one of these fields.
* 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 ... NOTE
Packages in Depends field not imported from:
  ‘BMA’ ‘leaps’ ‘splines’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
iterateBMAsurv.train: no visible global function definition for
  ‘bic.surv’
iterateBMAsurv.train.wrapper: no visible global function definition for
  ‘bic.surv’
Undefined global functions or variables:
  bic.surv
* checking Rd files ... WARNING
checkRd: (-1) crossVal.Rd:74: Escaped LaTeX specials: \_ \_ \_ \_
checkRd: (5) iterateBMAsurv.train.Rd:67-98: \item in \value must have non-empty label
prepare_Rd: predictBicSurv.Rd:46: Dropping empty section \note
prepare_Rd: predictiveAssessCategory.Rd:52: Dropping empty section \note
prepare_Rd: printTopGenes.Rd:49: Dropping empty section \note
checkRd: (-1) printTopGenes.Rd:22: Escaped LaTeX specials: \_ \_
prepare_Rd: singleGeneCoxph.Rd:54: Dropping empty section \note
checkRd: (-1) singleGeneCoxph.Rd:32: Escaped LaTeX specials: \_
prepare_Rd: testCens.Rd:13-14: Dropping empty section \details
prepare_Rd: testSurv.Rd:13-14: Dropping empty section \details
prepare_Rd: trainCens.Rd:13-14: Dropping empty section \details
prepare_Rd: trainSurv.Rd:13-14: Dropping empty section \details
* 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
Examples with CPU (user + system) or elapsed time > 5s
                               user system elapsed
imageplot.iterate.bma.surv   10.759  0.103  11.194
iterateBMAsurv.train          5.695  0.082   5.979
predictiveAssessCategory      5.444  0.098   5.560
predictBicSurv                5.315  0.062   5.422
iterateBMAsurv.train.wrapper  5.178  0.043   5.269
* 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 WARNING, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/iterativeBMAsurv.Rcheck/00check.log’
for details.

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘iterativeBMAsurv’ ...
** 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 (iterativeBMAsurv)