* using log directory '/home/kingaa/projects/Rpkg/subplex/revdep/DDD.Rcheck'
* using R version 4.2.2 (2022-10-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option '--as-cran'
* checking for file 'DDD/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'DDD' version '5.2.1'
* 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 executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'DDD' can be installed ... [105s/152s] OK
* checking installed package size ... NOTE
  installed size is 16.9Mb
  sub-directories of 1Mb or more:
    libs  16.4Mb
* checking package directory ... OK
* checking for future file timestamps ... 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 R 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 use of S3 registration ... 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 ... [30s/40s] NOTE
L2brts: local variable ‘daughter’ assigned but may not be used
L2phylo: local variable ‘daughter’ assigned but may not be used
bd_loglik: local variable ‘abstol’ assigned but may not be used
bd_loglik: local variable ‘reltol’ assigned but may not be used
check_for_impossible_pars_KI: local variable ‘loglik’ assigned but may
  not be used
dd_KI_loglik: local variable ‘S’ assigned but may not be used
dd_LR: local variable ‘inverse_quantile’ assigned but may not be used
dd_MS_loglik: local variable ‘lx2’ assigned but may not be used
dd_MS_loglik: local variable ‘tcrown’ assigned but may not be used
dd_MS_loglik: local variable ‘tpres’ assigned but may not be used
dd_SR_loglik2: local variable ‘abstol’ assigned but may not be used
dd_SR_loglik2: local variable ‘expMM1’ assigned but may not be used
dd_SR_loglik2: local variable ‘reltol’ assigned but may not be used
dd_bootstrap_sim: local variable ‘simout’ assigned but may not be used
dd_loglik2: local variable ‘abstol’ assigned but may not be used
dd_loglik2: local variable ‘reltol’ assigned but may not be used
td_loglik_rhs: local variable ‘sigdiv’ assigned but may not be used
td_loglik_rhs_sim: local variable ‘lrs’ assigned but may not be used
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... 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 line endings in C/C++/Fortran sources/headers ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking examples ... [67s/24s] OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
dd_SR_loglik 7.631 16.573   5.332
dd_loglik    5.811 12.836   4.175
dd_ML        2.536  5.388   3.282
dd_SR_ML     1.669  4.517   1.365
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
 [488s/160s] OK
* checking PDF version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 2 NOTEs
